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Proteins: Proteomics and Beyond
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Proteins: Proteomics and Beyond

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (20 October 2021) | Viewed by 24443

Special Issue Editors

Dr. Chandrasekhar Natarajan

E-Mail Website
Guest Editor
University of Nebraska-Lincoln, Lincoln, NE, USA
Interests: protein evolution; protein engineering; structure-function; evolutionary biochemistry; hemoglobin
Dr. Neetha Nanoth Vellichirammal

E-Mail Website
Guest Editor
University of Nebraska Medical Center, Omaha, NE, USA
Interests: high throughput proteomics; fusion genes; bioinformatics; cancer genetics; diagnostic protein markers; personalized medicine
Dr. Nishana Mayilaadumveettil

E-Mail Website
Guest Editor
New York University Langone Health, New York, USA
Interests: protein-protein interactions; protein-DNA complexes; chromosome architecture; genomics; regulation of gene expression

Special Issue Information

Dear Colleagues,

Recent technological advancements in mass spectrometry-based high-throughput proteomics have redefined the biomedical sciences and have played a key role in understanding human diseases. Proteins are the molecules that dictate the structure, function, metabolism, and signaling events in the cells. They also play a crucial role in prognosis, diagnosis, and drug responsiveness to a disease. Though cost-effective genome sequencing technologies have revolutionized and contributed efficiently towards discovering the novel biological processes, they alone do not capture these processes in their entirety. For example, despite the rapid detection of mutations in protein-coding genes, the impact of these mutations on the protein structure, function, and interacting protein partners or ligands has not been studied at a comparable pace.

The exponential advancements in high-throughput technologies complemented by advanced bioinformatics tools have resulted in a shift of paradigm from studying individual genes or proteins to the global “omics” discipline. While errors in proteins are a major cause of diseases, proteins can also cure diseases, since they serve as the most promising target for drugs to date. The roles they play in the disease-specific cellular circuitry cannot be exclusively attributed to the primary structure but are also impacted by spatio-temporal expression changes, folding, post-translational modifications, protein-protein, protein-DNA, and protein-ligand interactions, which can be deciphered with the help of proteomic tools. In turn, this has helped us unravel the dynamic processes of origin of diseases, thereby supporting early detection, classification, prognosis, diagnosis, and the development of personalized therapeutic combinations based on resistance and toxicity.

In this special issue of Genes on “Proteins: Proteomics and Beyond” we aim to compile a series of original and review articles focusing on experimental and theoretical approaches addressing the structure-function relationship, proteins or proteomic profiles in various biological systems, protein evolution, protein engineering and designs, molecular interactions (protein-protein or protein-ligand), protein folding, post-translational modification (PTM), and protein biomarkers.

Dr. Chandrasekhar Natarajan
Dr. Neetha Nanoth Vellichirammal
Dr. Nishana Mayilaadumveettil
Guest Editors

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • protein evolution 
  • structure-function 
  • protein complexes 
  • protein engineering 
  • proteomics 
  • diagnostic protein markers 
  • mutations 
  • protein variations 
  • post-translational modification

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Published Papers (7 papers)

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Research

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13 pages, 5744 KiB  
Article
Clinical Characteristics and In Silico Analysis of Cystinuria Caused by a Novel SLC3A1 Mutation
by Lexin Liu, Zihao Xu, Yuelin Guan, Ying Zhang, Xue Li, Yunqing Ren, Lidan Hu and Xiang Yan
Genes 2022, 13(11), 2173; https://doi.org/10.3390/genes13112173 - 21 Nov 2022
Viewed by 2041
Abstract
Cystinuria is a genetically inherited disorder of renal and intestinal transport, featured as a high concentration of cystine in the urine. Cumulative cystine in urine would cause the formation of kidney stones, which further leads to renal colic and dysfunction. Gene screens have [...] Read more.
Cystinuria is a genetically inherited disorder of renal and intestinal transport, featured as a high concentration of cystine in the urine. Cumulative cystine in urine would cause the formation of kidney stones, which further leads to renal colic and dysfunction. Gene screens have found that mutations in SLC3A1 or SLC7A9 gene are responsible for most cases of cystinuria, for encoding defective cystine transporters. Here, we presented the genotypic and phenotypic characteristics of one unique case of a three-generation Chinese family. The proband developed severe urolithiasis combined with renal damage. The radiography and computed tomography (CT) scan showed calculus in the left pelvic kidney. Postoperative stone analysis revealed that the stones were mainly composed of cystine. Therefore, to explore its pathogenesis, next-generation Whole Exome Sequencing (WES) and Sanger sequencing identify the proband mutated gene of the proband’s family. In this article, we reported novel compound heterozygous mutations (c.818G>A and c.1011G>A) of the SLC3A1 gene in a 5-year-old child suffering from a cystine stone from a three-generation family. Bioinformatic analysis was used to predict the pathogenicity and conservation of the target mutation. Conservative sequence and evolutionary conservation analysis indicated that cystine273 and proline337 were highly conserved among species, and both mutations listed here (Cys273Tyr and Pro337Pro) were pathogenic. To conclude, our study expands the phenotypic and genotypic spectrum of SLC3A1 and indicates that genetic screening should be considered in the clinic to provide more effective and precise treatment for cystinuria. Full article
(This article belongs to the Special Issue Proteins: Proteomics and Beyond)
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17 pages, 7871 KiB  
Article
A Quantitative Proteomics Approach to Gain Insight into NRF2-KEAP1 Skeletal Muscle System and Its Cysteine Redox Regulation
by Rafay Abu, Li Yu, Ashok Kumar, Lie Gao and Vikas Kumar
Genes 2021, 12(11), 1655; https://doi.org/10.3390/genes12111655 - 21 Oct 2021
Cited by 5 | Viewed by 3173
Abstract
Mammalian skeletal muscle (SkM) tissue engages the Nrf2-Keap1-dependent antioxidant defense mechanism to respond adaptively to stress. Redox homeostasis mediated by the reversible modification of selective cysteines is the prevalent mode of regulation. The protein targets of SkM redox regulation are largely unknown. We [...] Read more.
Mammalian skeletal muscle (SkM) tissue engages the Nrf2-Keap1-dependent antioxidant defense mechanism to respond adaptively to stress. Redox homeostasis mediated by the reversible modification of selective cysteines is the prevalent mode of regulation. The protein targets of SkM redox regulation are largely unknown. We previously reported the proteomic profiles of soleus (Sol) and extensor digitorum longus (EDL) with Nrf2 or Keap1 gene deletion, using SkM-specific Nrf2 or Keap1 knockout models; iMS-Nrf2flox/flox; and iMS-Keap1flox/flox. Here, we employed these two animal models to understand the global expression profile of red tibialis anterior (RTA) using a label free approach and its redox proteomics using iodoacetyl tandem mass tag (iodoTMTTM)-labeled cysteine quantitation. We quantified 298 proteins that were significantly altered globally in the RTA with Nrf2 deficiency but only 21 proteins in the Keap1 KO samples. These proteins are involved in four intracellular signaling pathways: sirtuin signaling, Nrf2 mediated oxidative stress response, oxidative phosphorylation, and mitochondrion dysfunction. Moreover, we identified and quantified the cysteine redox peptides of 34 proteins, which are associated with mitochondrial oxidative phosphorylation, energy metabolism, and extracellular matrix. Our findings suggest that Nrf2-deficient RTA is implicated in metabolic myopathy, mitochondrial disorders, and motor dysfunction, possibly due to an enhanced oxidative modification of the structure and functional proteins in skeletal myocytes. Full article
(This article belongs to the Special Issue Proteins: Proteomics and Beyond)
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15 pages, 5061 KiB  
Article
A Genome-Wide Analysis of Pathogenesis-Related Protein-1 (PR-1) Genes from Piper nigrum Reveals Its Critical Role during Phytophthora capsici Infection
by Divya Kattupalli, Asha Srinivasan and Eppurath Vasudevan Soniya
Genes 2021, 12(7), 1007; https://doi.org/10.3390/genes12071007 - 30 Jun 2021
Cited by 27 | Viewed by 4471
Abstract
Black pepper (Piper nigrum L.) is a prominent spice that is an indispensable ingredient in cuisine and traditional medicine. Phytophthora capsici, the causative agent of footrot disease, causes a drastic constraint in P. nigrum cultivation and productivity. To counterattack various biotic [...] Read more.
Black pepper (Piper nigrum L.) is a prominent spice that is an indispensable ingredient in cuisine and traditional medicine. Phytophthora capsici, the causative agent of footrot disease, causes a drastic constraint in P. nigrum cultivation and productivity. To counterattack various biotic and abiotic stresses, plants employ a broad array of mechanisms that includes the accumulation of pathogenesis-related (PR) proteins. Through a genome-wide survey, eleven PR-1 genes that belong to a CAP superfamily protein with a caveolin-binding motif (CBM) and a CAP-derived peptide (CAPE) were identified from P. nigrum. Despite the critical functional domains, PnPR-1 homologs differ in their signal peptide motifs and core amino acid composition in the functional protein domains. The conserved motifs of PnPR-1 proteins were identified using MEME. Most of the PnPR-1 proteins were basic in nature. Secondary and 3D structure analyses of the PnPR-1 proteins were also predicted, which may be linked to a functional role in P. nigrum. The GO and KEGG functional annotations predicted their function in the defense responses of plant-pathogen interactions. Furthermore, a transcriptome-assisted FPKM analysis revealed PnPR-1 genes mapped to the P. nigrum-P. capsici interaction pathway. An altered expression pattern was detected for PnPR-1 transcripts among which a significant upregulation was noted for basic PnPR-1 genes such as CL10113.C1 and Unigene17664. The drastic variation in the transcript levels of CL10113.C1 was further validated through qRT-PCR and it showed a significant upregulation in infected leaf samples compared with the control. A subsequent analysis revealed the structural details, phylogenetic relationships, conserved sequence motifs and critical cis-regulatory elements of PnPR-1 genes. This is the first genome-wide study that identified the role of PR-1 genes during P. nigrum-P. capsici interactions. The detailed in silico experimental analysis revealed the vital role of PnPR-1 genes in regulating the first layer of defense towards a P. capsici infection in Panniyur-1 plants. Full article
(This article belongs to the Special Issue Proteins: Proteomics and Beyond)
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11 pages, 3268 KiB  
Article
Proteomics Analysis Reveals Diverse Molecular Characteristics between Endocardial and Aortic-Valvular Endothelium
by A. Aneesh Kumar, G. S. Ajith Kumar, Gopika Satheesh, Arun Surendran, Mahesh Chandran, Chandrasekharan C. Kartha and Abdul Jaleel
Genes 2021, 12(7), 1005; https://doi.org/10.3390/genes12071005 - 30 Jun 2021
Cited by 6 | Viewed by 2764
Abstract
The variations in the protein profile of aortic-valvular (AVE) and endocardial endothelial (EE) cells are currently unknown. The current study’s objective is to identify differentially expressed proteins and associated pathways in both the endothelial cells. We used endothelial cells isolated from the porcine [...] Read more.
The variations in the protein profile of aortic-valvular (AVE) and endocardial endothelial (EE) cells are currently unknown. The current study’s objective is to identify differentially expressed proteins and associated pathways in both the endothelial cells. We used endothelial cells isolated from the porcine (Sus scrofa) aortic valve and endocardium for the profiling of proteins. Label-free proteomics was performed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Our proteomics analysis revealed that 29 proteins were highly expressed, and 25 proteins were less expressed in the valve than the endocardial endothelium. The cell surface markers, such as CD63, ICAM1, PECAM1, PROCR, and TFRC, were highly expressed in EE. In contrast, CD44 was highly expressed in AVE. The pathway analysis showed that metabolic process-related proteins and extracellular matrix-related proteins were enriched in valves. Differential enrichment of signaling pathways was observed in the endocardium. The hemostasis function-related proteins were increased in both endothelial cells. The proteins and pathways enriched in aortic-valvular and endocardial endothelial cells revealed the distinct phenotype of these two closely related cells. Full article
(This article belongs to the Special Issue Proteins: Proteomics and Beyond)
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14 pages, 16572 KiB  
Article
α-Fodrin in Cytoskeletal Organization and the Activity of Certain Key Microtubule Kinesins
by Jamuna S. Sreeja, Athira Jyothy and Suparna Sengupta
Genes 2021, 12(5), 750; https://doi.org/10.3390/genes12050750 - 17 May 2021
Cited by 3 | Viewed by 2893
Abstract
Cortical cytoskeletal proteins are significant in controlling various cellular mechanisms such as migration, cell adhesion, intercellular attachment, cellular signaling, exo- and endocytosis and plasma membrane integrity, stability and flexibility. Our earlier studies involving in vitro and ex vivo approaches led us to identify [...] Read more.
Cortical cytoskeletal proteins are significant in controlling various cellular mechanisms such as migration, cell adhesion, intercellular attachment, cellular signaling, exo- and endocytosis and plasma membrane integrity, stability and flexibility. Our earlier studies involving in vitro and ex vivo approaches led us to identify certain undiscovered characteristics of α-fodrin, a prominent cortical protein. The conventional functions attributed to this protein mainly support the plasma membrane. In the present study, we utilized a global protein expression analysis approach to detect underexplored functions of this protein. We report that downregulation of α-fodrin in glioblastoma cells, U-251 MG, results in upregulation of genes affecting the regulation of the cytoskeleton, cell cycle and apoptosis. Interestingly, certain key microtubule kinesins such as KIF23, KIF2B and KIF3C are downregulated upon α-fodrin depletion, as validated by real-time PCR studies. Full article
(This article belongs to the Special Issue Proteins: Proteomics and Beyond)
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15 pages, 1895 KiB  
Article
Mitochondrial Processes during Early Development of Dictyostelium discoideum: From Bioenergetic to Proteomic Studies
by Monika Mazur, Daria Wojciechowska, Ewa Sitkiewicz, Agata Malinowska, Bianka Świderska, Hanna Kmita and Małgorzata Wojtkowska
Genes 2021, 12(5), 638; https://doi.org/10.3390/genes12050638 - 25 Apr 2021
Cited by 4 | Viewed by 2640
Abstract
The slime mold Dictyostelium discoideum’s life cycle includes different unicellular and multicellular stages that provide a convenient model for research concerning intracellular and intercellular mechanisms influencing mitochondria’s structure and function. We aim to determine the differences between the mitochondria isolated from the slime [...] Read more.
The slime mold Dictyostelium discoideum’s life cycle includes different unicellular and multicellular stages that provide a convenient model for research concerning intracellular and intercellular mechanisms influencing mitochondria’s structure and function. We aim to determine the differences between the mitochondria isolated from the slime mold regarding its early developmental stages induced by starvation, namely the unicellular (U), aggregation (A) and streams (S) stages, at the bioenergetic and proteome levels. We measured the oxygen consumption of intact cells using the Clarke electrode and observed a distinct decrease in mitochondrial coupling capacity for stage S cells and a decrease in mitochondrial coupling efficiency for stage A and S cells. We also found changes in spare respiratory capacity. We performed a wide comparative proteomic study. During the transition from the unicellular stage to the multicellular stage, important proteomic differences occurred in stages A and S relating to the proteins of the main mitochondrial functional groups, showing characteristic tendencies that could be associated with their ongoing adaptation to starvation following cell reprogramming during the switch to gluconeogenesis. We suggest that the main mitochondrial processes are downregulated during the early developmental stages, although this needs to be verified by extending analogous studies to the next slime mold life cycle stages. Full article
(This article belongs to the Special Issue Proteins: Proteomics and Beyond)
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Review

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21 pages, 1053 KiB  
Review
Applications of CRISPR-Cas Technologies to Proteomics
by Georgii Dolgalev and Ekaterina Poverennaya
Genes 2021, 12(11), 1790; https://doi.org/10.3390/genes12111790 - 12 Nov 2021
Cited by 6 | Viewed by 5188
Abstract
CRISPR-Cas-based genome editing is a revolutionary approach that has provided an unprecedented investigational power for the life sciences. Rapid and efficient, CRISPR-Cas technologies facilitate the generation of complex biological models and at the same time provide the necessary methods required to study these [...] Read more.
CRISPR-Cas-based genome editing is a revolutionary approach that has provided an unprecedented investigational power for the life sciences. Rapid and efficient, CRISPR-Cas technologies facilitate the generation of complex biological models and at the same time provide the necessary methods required to study these models in depth. The field of proteomics has already significantly benefited from leveraging the power of CRISPR-Cas technologies, however, many potential applications of these technologies in the context of proteomics remain unexplored. In this review, we intend to provide an introduction to the CRISPR-Cas technologies and demonstrate how they can be applied to solving proteome-centric questions. To achieve this goal, we begin with the description of the modern suite of CRISPR-Cas-based tools, focusing on the more mature CRISPR-Cas9 system. In the second part of this review, we highlight both established and potential applications of the CRISPR-Cas technologies to proteomics. Full article
(This article belongs to the Special Issue Proteins: Proteomics and Beyond)
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