scholarly journals MetaLab 2.0 enables accurate post-translational modifications profiling in metaproteomics

2019 ◽  
Author(s):  
Kai Cheng ◽  
Zhibin Ning ◽  
Xu Zhang ◽  
Leyuan Li ◽  
Bo Liao ◽  
...  
Keyword(s):  
Data Analysis ◽  
Microbial Communities ◽  
Search Strategy ◽  
Structure And Function ◽  
Research Field ◽  
Human Gut ◽  
Post Translational Modifications ◽  
Protein Functions ◽  
And Function

AbstractStudying the structure and function of microbiomes is an emerging research field. Metaproteomic approaches focusing on the characterization of expressed proteins and post-translational modifications (PTMs) provide a deeper understanding of microbial communities. Previous research has highlighted the value of examining microbiome-wide protein expression in studying the roles of the microbiome in human diseases. Nevertheless, the regulation of protein functions in complex microbiomes remains under-explored. This is mainly due to the lack of efficient bioinformatics tools to identify and quantify PTMs in the microbiome. We have developed a comprehensive software termed MetaLab for the data analysis of metaproteomic datasets. Here we build an open search workflow within MetaLab for unbiased identification and quantification of PTMs from microbiome samples. This bioinformatics platform provides information about proteins, PTMs, taxa, functions, and pathways of microbial communities. The performance of the workflow was evaluated using conventional proteomics, metaproteomics from mouse and human gut microbiomes, and modification-specific enriched datasets. Superior accuracy and sensitivity were obtained simultaneously by using our method comparing with the traditional closed search strategy.

scholarly journals Exploring the microbiome-wide lysine acetylation, succinylation and propionylation in human gut microbiota

2020 ◽  
Author(s):  
Xu Zhang ◽  
Kai Cheng ◽  
Zhibin Ning ◽  
Janice Mayne ◽  
Krystal Walker ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Search Strategy ◽  
Analytical Framework ◽  
Database Search ◽  
Lysine Acetylation ◽  
Cellular Functions ◽  
Human Gut ◽  
Post Translational Modifications ◽  
Translational Level

AbstractBackgroundLysine acylations are important post-translational modifications that are present in both eukaryotes and prokaryotes, regulating diverse cellular functions. Our knowledge of the microbiome lysine acylation remains limited due to the lack of efficient analytical and bioinformatics methods for complex microbial communities.ResultsWe show that serial enrichment using motif antibodies successfully captures peptides containing lysine acetylation, propionylation and succinylation from human gut microbiome samples. A new bioinformatic workflow consisting of unrestricted database search confidently identified >60,000 acetylated, and ~20,000 propionylated and succinylated gut microbial peptides. Characterization of these identified modification-specific metaproteomes, i.e. meta-PTMomes, demonstrates that lysine acylations are differentially distributed in microbial species with different metabolic capabilities.ConclusionThis study provides an analytical framework, consisting of a serial immunoaffinity enrichment and an open database search strategy, for the study of lysine acylations in microbiome, which enables functional microbiome studies at the post-translational level.

scholarly journals A Rubisco-binding protein is required for normal pyrenoid number and starch sheath morphology inChlamydomonas reinhardtii

2019 ◽  
Vol 116 (37) ◽  
pp. 18445-18454 ◽  
Author(s):  
Alan K. Itakura ◽  
Kher Xing Chan ◽  
Nicky Atkinson ◽  
Leif Pallesen ◽  
Lianyong Wang ◽  
...  
Keyword(s):  
Surface Area ◽  
Structure And Function ◽  
Binding Motif ◽  
Starch Granules ◽  
Wild Type ◽  
Bisphosphate Carboxylase ◽  
Biophysical Mechanism ◽  
Mechanism Function ◽  
And Function

A phase-separated, liquid-like organelle called the pyrenoid mediates CO2fixation in the chloroplasts of nearly all eukaryotic algae. While most algae have 1 pyrenoid per chloroplast, here we describe a mutant in the model algaChlamydomonasthat has on average 10 pyrenoids per chloroplast. Characterization of the mutant leads us to propose a model where multiple pyrenoids are favored by an increase in the surface area of the starch sheath that surrounds and binds to the liquid-like pyrenoid matrix. We find that the mutant’s phenotypes are due to disruption of a gene, which we call StArch Granules Abnormal 1 (SAGA1) because starch sheath granules, or plates, in mutants lacking SAGA1 are more elongated and thinner than those of wild type. SAGA1 contains a starch binding motif, suggesting that it may directly regulate starch sheath morphology. SAGA1 localizes to multiple puncta and streaks in the pyrenoid and physically interacts with the small and large subunits of the carbon-fixing enzyme Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase), a major component of the liquid-like pyrenoid matrix. Our findings suggest a biophysical mechanism by which starch sheath morphology affects pyrenoid number and CO2-concentrating mechanism function, advancing our understanding of the structure and function of this biogeochemically important organelle. More broadly, we propose that the number of phase-separated organelles can be regulated by imposing constraints on their surface area.

scholarly journals Characterization of splice variants of human caspase-activated DNase with CIDE-N structure and function

FEBS Letters ◽  
2004 ◽  
Vol 566 (1-3) ◽  
pp. 234-240 ◽  
Author(s):  
José R. Bayascas ◽  
Vı́ctor J. Yuste ◽  
Carme Solé ◽  
Isabel Sánchez-López ◽  
Miquel F. Segura ◽  
...  
Keyword(s):  
Splice Variants ◽  
Structure And Function ◽  
Caspase Activated Dnase ◽  
And Function ◽  
Human Caspase

scholarly journals The Structure and Function of Healing And Charm Spells

2020 ◽  
Vol 1 (2) ◽  
pp. 193-208
Author(s):  
Andri Asmara ◽  
Yessi Fitriani ◽  
Arif Ardiansyah
Keyword(s):  
Content Analysis ◽  
Data Analysis ◽  
Structure And Function ◽  
Qualitative Descriptive ◽  
Opposite Sex ◽  
And Function ◽  
Descriptive Method

This study aimed to determine the structure and function of healing and charm spells in Makarti Jaya village, Banyuasin District. This research used a qualitative descriptive method. The source of the data was 22 healing and charm spells which are taken from three informants. The data analysis used was content analysis. The results of this study indicated that not all spells mention a name component because some spells do not have a name element but still do not reduce the magical value of the spell, for a name is not a measure of whether the spell is effective. In the component of the opening greeting, The suggestions received in the analyzed spell are aimed at making the spell look pleasing. In the objective component, all spells have the same goal, which is to captivate the opposite sex. Whereas the closing element of all spells uses words from Arabic such as laillahailallah muhamadarasulullah. From the analysis of the seven healing spells and fifteen charm spells, it showed that the spell has a different structure and function according to the verse contained in the spell.

scholarly journals Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
A.E. Naas ◽  
A.K. MacKenzie ◽  
B. Dalhus ◽  
V.G.H. Eijsink ◽  
P.B. Pope
Keyword(s):  
Active Site ◽  
Three Dimensional ◽  
Structural Features ◽  
Structure And Function ◽  
Dimensional Structure ◽  
Active Site Cleft ◽  
Polysaccharide Utilization Locus ◽  
And Function ◽  
Rumen Metagenome

Abstract Previous gene-centric analysis of a cow rumen metagenome revealed the first potentially cellulolytic polysaccharide utilization locus, of which the main catalytic enzyme (AC2aCel5A) was identified as a glycoside hydrolase (GH) family 5 endo-cellulase. Here we present the 1.8 Å three-dimensional structure of AC2aCel5A and characterization of its enzymatic activities. The enzyme possesses the archetypical (β/α)8-barrel found throughout the GH5 family and contains the two strictly conserved catalytic glutamates located at the C-terminal ends of β-strands 4 and 7. The enzyme is active on insoluble cellulose and acts exclusively on linear β-(1,4)-linked glucans. Co-crystallization of a catalytically inactive mutant with substrate yielded a 2.4 Å structure showing cellotriose bound in the −3 to −1 subsites. Additional electron density was observed between Trp178 and Trp254, two residues that form a hydrophobic “clamp”, potentially interacting with sugars at the +1 and +2 subsites. The enzyme’s active-site cleft was narrower compared to the closest structural relatives, which in contrast to AC2aCel5A, are also active on xylans, mannans and/or xyloglucans. Interestingly, the structure and function of this enzyme seem adapted to less-substituted substrates such as cellulose, presumably due to the insufficient space to accommodate the side-chains of branched glucans in the active-site cleft.

scholarly journals Conservation of dishevelled structure and function between flies and mice: isolation and characterization of Dvl2

1996 ◽  
Vol 58 (1-2) ◽  
pp. 15-26 ◽  
Author(s):  
J. Klingensmith ◽  
Y. Yang ◽  
J.D. Axelrod ◽  
D.R. Beier ◽  
N. Perrimon ◽  
...  
Keyword(s):  
Structure And Function ◽  
Isolation And Characterization ◽  
And Function
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