A Novel Thioredoxin-Dependent Peroxiredoxin (TPx-Q) Plays an Important Role in Defense Against Oxidative Stress and Is a Possible Drug Target in Babesia microti

Zhang, Houshuang; Wang, Zhonghua; Huang, Jingsheng; Cao, Jie; Zhou, Yongzhi; Zhou, Jinlin

doi:10.3389/fvets.2020.00076

Cited by 12 publications

(4 citation statements)

References 62 publications

(84 reference statements)

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“…It was suggested that peptidylprolyl isomerases have a role in abiotic stress response in plants 69 . In addition, thioredoxin-dependent peroxiredoxin as part of antioxidant defenses and redox signaling is essential for cellular response against oxidative stress 70 . Previous observation implies a possible link between mitochondrial thioredoxin system and peptidyl prolyl cis –trans isomerase activity 71 .…”

Section: Discussionmentioning

confidence: 99%

Integration of meta-analysis, machine learning and systems biology approach for investigating the transcriptomic response to drought stress in Populus species

Tahmasebi

Niazi‎

Akrami

2023

Sci Rep

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In Populus, drought is a major problem affecting plant growth and development which can be closely reflected by corresponding transcriptomic changes. Nevertheless, how these changes in Populus are not fully understood. Here, we first used meta-analysis and machine learning methods to identify water stress-responsive genes and then performed a systematic approach to discover important gene networks. Our analysis revealed that large transcriptional variations occur during drought stress. These changes were more associated with the response to stress, cellular catabolic process, metabolic pathways, and hormone-related genes. The differential gene coexpression analysis highlighted two acetyltransferase NATA1-like and putative cytochrome P450 genes that have a special contribution in response to drought stress. In particular, the findings showed that MYBs and MAPKs have a prominent role in the drought stress response that could be considered to improve the drought tolerance of Populus. We also suggest ARF2-like and PYL4-like genes as potential markers for use in breeding programs. This study provides a better understanding of how Populus responses to drought that could be useful for improving tolerance to stress in Populus.

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Section: Discussionmentioning

confidence: 99%

Integration of meta-analysis, machine learning and systems biology approach for investigating the transcriptomic response to drought stress in Populus species

Tahmasebi

Niazi‎

Akrami

2023

Sci Rep

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“…As the O 2 diffuses in all directions the parasite lives in the line of fire. During the brief bouts of high O 2 partial pressure oxidative damage may occur to many components, perhaps exacerbated by hemoglobin peroxidase activity and associated radicals ( Reeder, 2017 ; Zhang et al., 2020 ). It is clear that appreciable oxidative damage occurs, based upon the accumulation of the lipid oxidation product, malondialdehyde, in IE membranes and fragmentation of DNA ( Commins et al., 1988 ; Murase et al., 1996 ; Esmaeilnejad et al., 2020 ), challenging parasite genome integrity.…”

Section: Why Cytoadhesion?mentioning

confidence: 99%

“…Malondialdehyde is itself carcinogenic, forming DNA base adducts ( Marnett, 2000 ). Damage generated by reactive oxygen species or nitrosylation from innate immune responses also would contribute to selective pressure ( Asada et al., 2015 ; Zhang et al., 2020 ). Cytoadhesive parasites avoid both clearance by the spleen and genotoxic damage from O 2 acquired in the lungs.…”

Section: Why Cytoadhesion?mentioning

confidence: 99%

Integration of DNA Repair, Antigenic Variation, Cytoadhesion, and Chance in Babesia Survival: A Perspective

Allred

2022

Front. Cell. Infect. Microbiol.

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Apicomplexan parasites live in hostile environments in which they are challenged chemically and their hosts attempt in many ways to kill them. In response, the parasites have evolved multiple mechanisms that take advantage of these challenges to enhance their survival. Perhaps the most impressive example is the evolutionary co-option of DNA repair mechanisms by the parasites as a means to rapidly manipulate the structure, antigenicity, and expression of the products of specific multigene families. The purpose of variant proteins that mediate cytoadhesion has long been thought to be primarily the avoidance of splenic clearance. Based upon known biology, I present an alternative perspective in which it is survival of the oxidative environment within which Babesia spp. parasites live that has driven integration of DNA repair, antigenic variation, and cytoadhesion, and speculate on how genome organization affects that integration. This perspective has ramifications for the development of parasite control strategies.

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“…It used a tripartite graph by including, in addition to the relationship between peptides and proteins, the connection between genes. He et al designed a linear programming model for protein ADY34425 thioredoxin peroxidase [55] https://doi.org/10.1371/journal.pcbi.1010603.t007…”

Section: Relation To the Existing Workmentioning

confidence: 99%

MetaLP: An integrative linear programming method for protein inference in metaproteomics

Feng

Ji²,

Wang³

et al. 2022

PLoS Comput Biol

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Metaproteomics based on high-throughput tandem mass spectrometry (MS/MS) plays a crucial role in characterizing microbiome functions. The acquired MS/MS data is searched against a protein sequence database to identify peptides, which are then used to infer a list of proteins present in a metaproteome sample. While the problem of protein inference has been well-studied for proteomics of single organisms, it remains a major challenge for metaproteomics of complex microbial communities because of the large number of degenerate peptides shared among homologous proteins in different organisms. This challenge calls for improved discrimination of true protein identifications from false protein identifications given a set of unique and degenerate peptides identified in metaproteomics. MetaLP was developed here for protein inference in metaproteomics using an integrative linear programming method. Taxonomic abundance information extracted from metagenomics shotgun sequencing or 16s rRNA gene amplicon sequencing, was incorporated as prior information in MetaLP. Benchmarking with mock, human gut, soil, and marine microbial communities demonstrated significantly higher numbers of protein identifications by MetaLP than ProteinLP, PeptideProphet, DeepPep, PIPQ, and Sipros Ensemble. In conclusion, MetaLP could substantially improve protein inference for complex metaproteomes by incorporating taxonomic abundance information in a linear programming model.

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A Novel Thioredoxin-Dependent Peroxiredoxin (TPx-Q) Plays an Important Role in Defense Against Oxidative Stress and Is a Possible Drug Target in Babesia microti

Cited by 12 publications

References 62 publications

Integration of meta-analysis, machine learning and systems biology approach for investigating the transcriptomic response to drought stress in Populus species

Integration of meta-analysis, machine learning and systems biology approach for investigating the transcriptomic response to drought stress in Populus species

Integration of DNA Repair, Antigenic Variation, Cytoadhesion, and Chance in Babesia Survival: A Perspective

MetaLP: An integrative linear programming method for protein inference in metaproteomics

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