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Sun HY, Ma YY, Cao XQ, Li H, Han W, Qu LJ, Lamont SJ. PTEN regulated by gga-miR-20a-5p is involved in chicken macrophages inflammatory response to APEC infection via autophagy. Poult Sci 2024; 103:104170. [PMID: 39154611 PMCID: PMC11381812 DOI: 10.1016/j.psj.2024.104170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/23/2024] [Accepted: 07/31/2024] [Indexed: 08/20/2024] Open
Abstract
Colibacillosis, a bacterial disease caused by avian pathogenic E. coli (APEC), is a prevalent condition in the poultry industry, resulting in substantial economic losses annually. Previously, we identified PTEN as a crucial candidate gene that may play a significant role in chicken's immune response to APEC infection. Bioinformatics analysis indicated that the PTEN protein was unstable, hydrophilic and nuclear localization, with multiple putative phosphorylation sites and a high degree of similarity to duck and goose PTEN. Moreover, PTEN exhibited high expression levels in various tissues such as the stomach, cecum, small intestine, spleen, thymus, harderian gland, muscle, cerebrum, cerebellum, lung, and liver in comparison to heart tissue. Overexpression of PTEN resulted in a significant promotion of the expression level of pro-apoptosis genes and inflammatory mediators, as well as the production of NO, with or without APEC infection, which led to cellular injury. Furthermore, overexpression of PTEN was found to regulate the expression levels of autophagy related genes, regardless of APEC infection. Additionally, PTEN was a target gene of gga-miR-20a-5p and regulated by gga-miR-20a-5p upon APEC infection. Taken together, these findings establish a foundation for investigating the biological function of chicken PTEN, providing a potential target for future treatments against APEC infection as well as the breeding of genetically resistant poultry.
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Affiliation(s)
- Hong-Yan Sun
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Yu-Yi Ma
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xin-Qi Cao
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Huan Li
- Department of Food Science, School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou 225009, China
| | - Wei Han
- Department of Resource Conservation and Evaluation, The Poultry Research Institute of Chinese Academy of Agricultural Sciences, Yangzhou 225009, China
| | - Lu-Jiang Qu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100091, China
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
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2
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Souza Amado de Carvalho R, Rasel MSI, Khandelwal NK, Tomasiak TM. Cryo-EM reveals a phosphorylated R-domain envelops the NBD1 catalytic domain in an ABC transporter. Life Sci Alliance 2024; 7:e202402779. [PMID: 39209537 PMCID: PMC11361370 DOI: 10.26508/lsa.202402779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Many ATP-binding cassette transporters are regulated by phosphorylation on long and disordered loops which presents a challenge to visualize with structural methods. We have trapped an activated state of the regulatory domain (R-domain) of yeast cadmium factor 1 (Ycf1) by enzymatically enriching the phosphorylated state. A 3.23 Å cryo-EM structure reveals an R-domain structure with four phosphorylated residues and the position for the entire R-domain. The structure reveals key R-domain interactions including a bridging interaction between NBD1 and NBD2 and an interaction with the R-insertion, another regulatory region. We scanned these interactions by systematically replacing segments along the entire R-domain with scrambled combinations of alanine, glycine, and glutamine and probing function under cellular conditions that require the Ycf1 function. We find a close match with these interactions and interacting regions on our R-domain structure that points to the importance of most well-structured segments for function. We propose a model where the R-domain stabilizes a transport-competent state upon phosphorylation by enveloping NBD1 entirely.
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Affiliation(s)
| | - Md Shamiul Islam Rasel
- https://ror.org/03m2x1q45 Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Nitesh K Khandelwal
- https://ror.org/03m2x1q45 Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Thomas M Tomasiak
- https://ror.org/03m2x1q45 Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
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Guo J, Wang J, Zhang K, Yang Z, Li B, Pan Y, Yu H, Yu S, Abbas Raza SH, Kuraz Abebea B, Zan L. Molecular cloning of TPM3 gene in qinchuan cattle and its effect on myoblast proliferation and differentiation. Anim Biotechnol 2024; 35:2345238. [PMID: 38775564 DOI: 10.1080/10495398.2024.2345238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Tropomyosin 3 (TPM3) plays a significant role as a regulatory protein in muscle contraction, affecting the growth and development of skeletal muscles. Despite its importance, limited research has been conducted to investigate the influence of TPM3 on bovine skeletal muscle development. Therefore, this study revealed the role of TPM3 in bovine myoblast growth and development. This research involved conducting a thorough examination of the Qinchuan cattle TPM3 gene using bioinformatics tools to examine its sequence and structural characteristics. Furthermore, TPM3 expression was evaluated in various bovine tissues and cells using quantitative real-time polymerase chain reaction (qRT-PCR). The results showed that the coding region of TPM3 spans 855 bp, with the 161st base being the T base, encoding a protein with 284 amino acids and 19 phosphorylation sites. This protein demonstrated high conservation across species while displaying a predominant α-helix secondary structure despite being an unstable acidic protein. Notably, a noticeable increase in TPM3 expression was observed in the longissimus dorsi muscle and myocardium of calves and adult cattle. Expression patterns varied during different stages of myoblast differentiation. Functional studies that involved interference with TPM3 in Qinchuan cattle myoblasts revealed a very significantly decrease in S-phase cell numbers and EdU-positive staining (P < 0.01), and disrupted myotube morphology. Moreover, interference with TPM3 resulted in significantly (P < 0.05) or highly significantly (P < 0.01) decreased mRNA and protein levels of key proliferation and differentiation markers, indicating its role in the modulation of myoblast behavior. These findings suggest that TPM3 plays an essential role in bovine skeletal muscle growth by influencing myoblast proliferation and differentiation. This study provides a foundation for further exploration into the mechanisms underlying TPM3-mediated regulation of bovine muscle development and provides valuable insights that could guide future research directions as well as potential applications for livestock breeding and addressing muscle-related disorders.
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Affiliation(s)
- Juntao Guo
- College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Jianfang Wang
- College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Ke Zhang
- College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Zhimei Yang
- College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Bingzhi Li
- Yangling Vocational and Technical College, Yangling, China
| | - Yueting Pan
- College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Hengwei Yu
- College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Shengchen Yu
- College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Sayed Haidar Abbas Raza
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, China
| | - Belete Kuraz Abebea
- College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A and F University, Yangling, China
- National Beef Cattle Improvement Center, Yangling, China
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Putaporntip C, Kuamsab N, Jongwutiwes S. Natural selection on apical membrane antigen 1 (AMA1) of an emerging zoonotic malaria parasite Plasmodium inui. Sci Rep 2024; 14:23637. [PMID: 39384839 DOI: 10.1038/s41598-024-74785-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 09/30/2024] [Indexed: 10/11/2024] Open
Abstract
Apical membrane antigen 1 (AMA1) of malaria parasites plays an important role in host cell invasion. Antibodies to AMA1 can inhibit malaria merozoite invasion of erythrocytes while vaccine-induced specific cytotoxic T cell responses to this protein are associated with clinical protection. Polymorphisms in AMA1 of Plasmodium falciparum (PfAMA1) and P. vivax (PvAMA1) are of concern for vaccine development. To date, little is known about sequence diversity in ama1 of P. inui (Piama1), an emerging zoonotic malaria parasite. In this study, 80 complete Piama1 coding sequences were obtained from 57 macaques in Thailand that defined 60 haplotypes clustering in two phylogenetic lineages. In total, 74 nucleotide substitutions were identified and distributed unevenly across the gene. Blockwise analysis of the rates of synonymous (dS) and nonsynonymous (dN) nucleotide substitutions did not show a significant deviation from neutrality among Thai isolates. However, significantly negative Tajima's D values were detected in domain I and the loop region of domain II, implying purifying selection. Codon-based analysis of dN/dS has identified 12 and 14 codons under positive and negative selections, respectively. Meanwhile, 85 amino acid substitutions were identified among 80 Thai and 11 non-Thai PiAMA1 sequences. Of these, 48 substituted residues had a significant alteration in physicochemical properties, suggesting positive selection. More than half of these positively selected amino acids (32 of 48) corresponded to the predicted B-cell or T-cell epitopes, suggesting that selective pressure could be mediated by host immunity. Importantly, 14 amino acid substitutions were singletons and predicted to be deleterious that could be subject to ongoing purifying selection or elimination. Besides genetic drift and natural selection, intragenic recombination identified in domain II could generate sequence variation in Piama1. It is likely that malarial ama1 exhibits interspecies differences in evolutionary histories. Knowledge of the sequence diversity of the Piama1 locus further provides an evolutionary perspective of this important malaria vaccine candidate.
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Affiliation(s)
- Chaturong Putaporntip
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Napaporn Kuamsab
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Faculty of Health Science and Technology, Community Public Health Program, Southern College of Technology, Nakorn Si Thammarat, Thailand
| | - Somchai Jongwutiwes
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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Wang B, Subramaniam S, Tian D, Mahsoub HM, Heffron CL, Meng XJ. Phosphorylation of Ser711 residue in the hypervariable region of zoonotic genotype 3 hepatitis E virus is important for virus replication. mBio 2024:e0263524. [PMID: 39377575 DOI: 10.1128/mbio.02635-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Accepted: 09/10/2024] [Indexed: 10/09/2024] Open
Abstract
Hepatitis E virus (HEV) is distinct from other hepatotropic viruses because it is zoonotic. HEV-1 and HEV-2 exclusively infect humans, whereas HEV-3 and HEV-4 are zoonotic. However, the viral and/or host factors responsible for cross-species HEV transmission remain elusive. The hypervariable region (HVR) in HEV is extremely heterogenetic and is implicated in HEV adaptation. Here, we investigated the potential role of Serine phosphorylation in the HVR in HEV replication. We first analyzed HVR sequences across different HEV genotypes and identified a unique region at the N-terminus of the HVR, which is variable in the human-exclusive HEV genotypes but relatively conserved in zoonotic HEV genotypes. Using predictive tools, we identified four potential phosphorylation sites that are highly conserved in zoonotic HEV-3 and HEV-4 genomes but absent in human-exclusive HEV-1 strains. To explore the functional significance of these putative phosphorylation sites, we introduced mutations into the HEV-3 infectious clone and indicator replicon, replacing each Serine residue individually with alanine or aspartic acid, and assessed the impact of these substitutions on HEV-3 replication. We found that the phospho-blatant S711A mutant significantly reduced virus replication, whereas the phospho-mimetic S711D mutant modestly reduced virus replication. Conversely, mutations in the other three Serine residues did not significantly affect HEV-3 replication. Furthermore, we demonstrated that Ser711 phosphorylation did not alter host cell tropism of zoonotic HEV-3. In conclusion, our results showed that potential phosphorylation of the Ser711 residue significantly affects HEV-3 replication in vitro, providing new insights into the potential mechanisms of zoonotic HEV transmission.IMPORTANCEHEV is an important zoonotic pathogen, causing both acute and chronic hepatitis E and extrahepatic manifestation of diseases, such as neurological sequelae. The zoonotic HEV-3 is linked to chronic infection and neurological diseases. The specific viral and/or host factors facilitating cross-species HEV infection are unknown. The intrinsically disordered HVR in ORF1 is crucial for viral fitness and adaptation, both in vitro and in vivo. We hypothesized that phosphorylation of Serine residues in the HVR of zoonotic HEV by unknown host cellular kinases is associated with cross-species HEV transmission. In this study, we identified a conserved region within the HVR of zoonotic HEV strains but absent in the human-exclusive HEV-1 and HEV-2. We elucidated the important role of phosphorylation at the Ser711 residue in zoonotic HEV-3 replication, without altering the host cell tropism. These findings contribute to our understanding the mechanisms of cross-species HEV transmission.
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Affiliation(s)
- Bo Wang
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
- Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Sakthivel Subramaniam
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
- Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Debin Tian
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
- Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Hassan M Mahsoub
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
- Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - C Lynn Heffron
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
- Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Xiang-Jin Meng
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
- Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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Lian C, Zhang B, Li J, Yang H, Liu X, Ma R, Zhang F, Liu J, Yang J, Lan J, Chen S. Genome-wide identification, characterization and expression pattern analysis of TIFY family members in Artemisia argyi. BMC Genomics 2024; 25:925. [PMID: 39363209 PMCID: PMC11451024 DOI: 10.1186/s12864-024-10856-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 09/30/2024] [Indexed: 10/05/2024] Open
Abstract
BACKGROUND Plant-specific TIFY proteins play crucial roles in regulating plant growth, development, and various stress responses. However, there is no information available about this family in Artemisia argyi, a well-known traditional medicinal plant with great economic value. RESULTS A total of 34 AaTIFY genes were identified, including 4 TIFY, 22 JAZ, 5 PPD, and 3 ZML genes. Structural, motif scanning, and phylogenetic relationships analysis of these genes revealed that members within the same group or subgroup exhibit similar exon-intron structures and conserved motif compositions. The TIFY genes were unevenly distributed across the 15 chromosomes. Tandem duplication events and segmental duplication events have been identified in the TIFY family in A. argyi. These events have played a crucial role in the gene multiplication and compression of different subfamilies within the TIFY family. Promoter analysis revealed that most AaTIFY genes contain multiple cis-elements associated with stress response, phytohormone signal transduction, and plant growth and development. Expression analysis of roots and leaves using RNA-seq data revealed that certain AaTIFY genes showed tissue-specific expression patterns, and some AaTIFY genes, such as AaTIFY19/29, were found to be involved in regulating salt and saline-alkali stresses. In addition, RT-qPCR analysis showed that TIFY genes, especially AaTIFY19/23/27/29, respond to a variety of hormonal treatments, such as MeJA, ABA, SA, and IAA. This suggested that TIFY genes in A. argyi regulate plant growth and respond to different stresses by following different hormone signaling pathways. CONCLUSION Taken together, our study conducted a comprehensive identification and analysis of the TIFY gene family in A. argyi. These findings suggested that TIFY might play an important role in plant development and stress responses, which laid a valuable foundation for further understanding the function of TIFY genes in multiple stress responses and phytohormone crosstalk in A. argyi.
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Affiliation(s)
- Conglong Lian
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou, 450046, PR China
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, Zhengzhou, 450046, PR China
- Collaborative Innovation Center of Research and Development on the Whole Industry Chain of Yu-Yao, Zhengzhou, Henan Province, 450046, PR China
| | - Bao Zhang
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou, 450046, PR China
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, Zhengzhou, 450046, PR China
| | - Jingjing Li
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou, 450046, PR China
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, Zhengzhou, 450046, PR China
| | - Hao Yang
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou, 450046, PR China
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, Zhengzhou, 450046, PR China
| | - Xiuyu Liu
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou, 450046, PR China
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, Zhengzhou, 450046, PR China
| | - Rui Ma
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou, 450046, PR China
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, Zhengzhou, 450046, PR China
| | - Fei Zhang
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou, 450046, PR China
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, Zhengzhou, 450046, PR China
| | - Jun Liu
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou, 450046, PR China
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, Zhengzhou, 450046, PR China
| | - Jingfan Yang
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou, 450046, PR China
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, Zhengzhou, 450046, PR China
| | - Jinxu Lan
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou, 450046, PR China.
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, Zhengzhou, 450046, PR China.
- Collaborative Innovation Center of Research and Development on the Whole Industry Chain of Yu-Yao, Zhengzhou, Henan Province, 450046, PR China.
| | - Suiqing Chen
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou, 450046, PR China.
- Henan Key Laboratory of Chinese Medicine Resources and Chemistry, Zhengzhou, 450046, PR China.
- Collaborative Innovation Center of Research and Development on the Whole Industry Chain of Yu-Yao, Zhengzhou, Henan Province, 450046, PR China.
- Co-Construction Collaborative Innovation Centre for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of China, Zhengzhou, 450046, PR China.
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Fodor I, Osugi T, Matsubara S, Shiraishi A, Kawada T, Pirger Z, Satake H. Characterization of corazonin signaling in a molluscan model species, Lymnaea stagnalis. Gen Comp Endocrinol 2024; 357:114594. [PMID: 39047798 DOI: 10.1016/j.ygcen.2024.114594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/10/2024] [Accepted: 07/20/2024] [Indexed: 07/27/2024]
Abstract
In recent years, new concepts have emerged regarding the nomenclature, functions, and relationships of different peptide families of the gonadotropin-releasing hormone (GnRH) superfamily. One of the main driving forces for this originated from the emerging evidence that neuropeptides previously called molluscan GnRH are multifunctional and should be classified as corazonin (CRZ). However, research articles still appear that use incorrect nomenclature and attribute the same function to molluscan CRZs as vertebrate GnRHs. The aim of the present study was to further support the recent interpretation of the origin and function of the GnRH superfamily. Towards this goal, we report the characterization of CRZ signaling system in the molluscan model species, the great pond snail (Lymnaea stagnalis). We detected a CRZ-receptor-like sequence (Lym-CRZR) by homology-searching in the Lymnaea transcriptomes and the deduced amino acid sequence showed high sequence similarity to GnRH receptors and CRZ receptors. Molecular phylogenetic tree analysis demonstrated that Lym-CRZR is included in the cluster of molluscan CRZRs. Lym-CRZR transiently transfected into HEK293 cells was found to be localized at the plasma membrane, confirming that it functions as a membrane receptor, like other G protein-coupled receptors. The signaling assays revealed that the previously identified Lym-CRZ neuropeptide stimulated intracellular Ca2+ mobilization in a dose-dependent manner, but not cyclic AMP production, in HEK293 cells transfected with Lym-CRZR. Finally, we demonstrated a wide tissue distribution of Lym-CRZR. These results suggest that Lym-CRZ is a multifunctional peptide and provide further insights into the evolution of the GnRH neuropeptide superfamily. The present study also supports the notion that previously termed molluscan "GnRH" should be classified as "CRZ".
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Affiliation(s)
- István Fodor
- Ecophysiological and Environmental Toxicological Research Group, HUN-REN Balaton Limnological Research Institute, Tihany 8237, Hungary.
| | - Tomohiro Osugi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Shin Matsubara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Akira Shiraishi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Tsuyoshi Kawada
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Zsolt Pirger
- Ecophysiological and Environmental Toxicological Research Group, HUN-REN Balaton Limnological Research Institute, Tihany 8237, Hungary
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
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Gang J, Ping Y, Du C. Anti-Magnaporthe oryzae Activity of Streptomyces bikiniensis HD-087 In Vitro and Bioinformatics Analysis of Polyketide Synthase Gene pksL. Curr Microbiol 2024; 81:379. [PMID: 39340701 DOI: 10.1007/s00284-024-03898-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 09/15/2024] [Indexed: 09/30/2024]
Abstract
Streptomyces bikiniensis HD-087 is capable of synthesizing various antimicrobial substances to counter the detrimental effects of hazardous microorganisms. To elucidate whether it produces polyketide antibiotics and the synthesis mechanism of antibiotic substances, the metabolites and related genes of S. bikiniensis HD-087 were analyzed through LC-MS, anti-Magnaporthe oryzae activity detection, and bioinformatics approaches. The result indicated that the strain HD-087 could produce erythromycin, a polyketide antibiotic. The inhibitory zones of the fermentation supernatant of strain HD-087 and methanol solution of erythromycin extract against M. oryzae were 40.84 ± 0.68 mm and 33.18 ± 0.81 mm, respectively. The IC50 value of erythromycin extract for inhibiting spore germination of erythromycin extract was 220.43 μg/mL. There are two polyketide synthesis gene clusters in the genome of strain HD-087, namely t1pks-nrps and t3pks-lantipeptide-t1pks-nrps. The key gene pksL in the t3pks-lantipeptide-t1pks-nrps gene cluster was predicted. The results suggested that it encodes a stable, hydrophilic, and acidic protein, mainly composed of α-helix and random coil. The PksL protein contains dehydrogenase (DH), ketone reductase (KR), acyl carrier protein (ACP), and ketone synthase (KS) domains. Moreover, it can form interaction networks with 11 proteins containing domains, such as polyketide synthase and ACP synthase. The molecular docking between PksL and acetyl-CoA is stable and strong, suggesting that PksL protein could catalyze the synthesis of polyketides with CoA as a substrate. This study provides a theoretical basis for further exploring the polyketides synthesis mechanism and developing antifungal metabolites in S. bikiniensis HD-087.
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Affiliation(s)
- Jiahan Gang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Yuan Ping
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Chunmei Du
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, 150080, China.
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Fan Y, He Y, Li Y, Yin Z, Shi J, Tian T, Shang K, Shi H, Zhang F, Wen H. Design of a novel EmTSP-3 and EmTIP based multi-epitope vaccine against Echinococcus multilocularis infection. Front Immunol 2024; 15:1425603. [PMID: 39351224 PMCID: PMC11439721 DOI: 10.3389/fimmu.2024.1425603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/20/2024] [Indexed: 10/04/2024] Open
Abstract
Background Current treatments and prevention strategies for echinococcosis are inadequate. Recent advancements in molecular vaccine development show promise against Echinococcus granulosus; however, Echinococcus multilocularis remains a challenge. A Multi-epitope Vaccine could potentially induce specific B and T lymphocyte responses, thereby offering protection against Echinococcus multilocularis infection. Methods This study aimed to develop a MEV against alveolar echinococcosis. Key epitopes from the Echinococcus multilocularis proteins EmTSP3 and EmTIP were identified using immunoinformatics analyses. These analyses were conducted to assess the MEV feasibility, structural characteristics, molecular docking, molecular dynamics simulations, and immune simulations. The immunogenicity and antigenicity of the vaccine were evaluated through in vitro and in vivo experiments, employing ELISA, Western blotting, FCM, challenge infection experiments, and ELISPOT. Results The effective antigenicity and immunogenicity of MEV were demonstrated through immunoinformatics, as well as in vitro and in vivo experiments. In vitro experiments revealed that MEV increased the secretion of IFN-γ and IL-4 in PBMC and successfully bound to specific antibodies in patient serum. Furthermore, mice immunized with MEV developed a robust immune response, characterized by elevated levels of CD4+ and CD8+ T-cells, increased secretion of IFN-γ and IL-4 by specific Th1 and Th2 cells, and heightened serum antibody levels. Importantly, MEV reduced the weight of cysts by conferring resistance against echinococcosis. These findings suggest that MEV is a promising candidate for the prevention of Echinococcus multilocularis infection. Conclusion A total of 7 CTL, 7 HTL, 5 linear B-cell, and 2 conformational B-cell epitopes were identified. The vaccine has demonstrated effective antigenicity and immunogenicity against AE through molecular docking, immune simulation, molecular dynamics studies, and both in vitro and in vivo experiments. It provides effective protection against Echinococcus multilocularis infection, thereby laying a foundation for further development.
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Affiliation(s)
- Yichen Fan
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medicine Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yueyue He
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Yujiao Li
- Department of Blood Transfusion, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zhengwei Yin
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Juan Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Tingting Tian
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Kaiyu Shang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Huidong Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Fengbo Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medicine Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Hao Wen
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medicine Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
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10
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Uddin MM, Hossain MT, Hossain MA, Ahsan A, Shamim KH, Hossen MA, Rahman MS, Rahman MH, Ahmed K, Bui FM, Al-Zahrani FA. Unraveling the potential effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on the Protein structure and function of the human SLC30A8 gene on type 2 diabetes and colorectal cancer: An In silico approach. Heliyon 2024; 10:e37280. [PMID: 39296124 PMCID: PMC11408818 DOI: 10.1016/j.heliyon.2024.e37280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/21/2024] Open
Abstract
Background and aims The single nucleotide polymorphisms (SNPs) in SLC30A8 gene have been recognized as contributing to type 2 diabetes (T2D) susceptibility and colorectal cancer. This study aims to predict the structural stability, and functional impacts on variations in non-synonymous SNPs (nsSNPs) in the human SLC30A8 gene using various computational techniques. Materials and methods Several in silico tools, including SIFT, Predict-SNP, SNPs&GO, MAPP, SNAP2, PhD-SNP, PANTHER, PolyPhen-1,PolyPhen-2, I-Mutant 2.0, and MUpro, have been used in our study. Results After data analysis, out of 336 missenses, the eight nsSNPs, namely R138Q, I141N, W136G, I349N, L303R, E140A, W306C, and L308Q, were discovered by ConSurf to be in highly conserved regions, which could affect the stability of their proteins. Project HOPE determines any significant molecular effects on the structure and function of eight mutated proteins and the three-dimensional (3D) structures of these proteins. The two pharmacologically significant compounds, Luzonoid B and Roseoside demonstrate strong binding affinity to the mutant proteins, and they are more efficient in inhibiting them than the typical SLC30A8 protein using Autodock Vina and Chimera. Increased binding affinity to mutant SLC30A8 proteins has been determined not to influence drug resistance. Ultimately, the Kaplan-Meier plotter study revealed that alterations in SLC30A8 gene expression notably affect the survival rates of patients with various cancer types. Conclusion Finally, the study found eight highly deleterious missense nsSNPs in the SLC30A8 gene that can be helpful for further proteomic and genomic studies for T2D and colorectal cancer diagnosis. These findings also pave the way for personalized treatments using biomarkers and more effective healthcare strategies.
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Affiliation(s)
- Md Moin Uddin
- Department of Biotechnology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md Tanvir Hossain
- Department of Biotechnology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md Arju Hossain
- Department of Microbiology, Primeasia University, Banani, Dhaka 1213, Bangladesh
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Asif Ahsan
- Department of Biotechnology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Kamrul Hasan Shamim
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Md Arif Hossen
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Md Shahinur Rahman
- Department of Diabetes and Endocrinology, Pabna Diabetic Association Hospital, Pabna 6600, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh
| | - Kawsar Ahmed
- Department of Electrical and Computer Engineering, University of Saskatchewan, 57 Campus Drive, Saskatoon, SK, S7N 5A9, Canada
- Group of Biophotomatiχ, Department of Information and Communication Technology, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
- Health Informatics Research Lab, Department of Computer Science and Engineering, Daffodil International University, Daffodil Smart City (DSC), Birulia, Savar, Dhaka-1216, Bangladesh
| | - Francis M Bui
- Department of Electrical and Computer Engineering, University of Saskatchewan, 57 Campus Drive, Saskatoon, SK, S7N 5A9, Canada
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11
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Ahmed F, Sharma A, Shatabda S, Dehzangi I. DeepPhoPred: Accurate Deep Learning Model to Predict Microbial Phosphorylation. Proteins 2024. [PMID: 39239684 DOI: 10.1002/prot.26734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/27/2024] [Accepted: 07/15/2024] [Indexed: 09/07/2024]
Abstract
Phosphorylation is a substantial posttranslational modification of proteins that refers to adding a phosphate group to the amino acid side chain after translation process in the ribosome. It is vital to coordinate cellular functions, such as regulating metabolism, proliferation, apoptosis, subcellular trafficking, and other crucial physiological processes. Phosphorylation prediction in a microbial organism can assist in understanding pathogenesis and host-pathogen interaction, drug and antibody design, and antimicrobial agent development. Experimental methods for predicting phosphorylation sites are costly, slow, and tedious. Hence low-cost and high-speed computational approaches are highly desirable. This paper presents a new deep learning tool called DeepPhoPred for predicting microbial phospho-serine (pS), phospho-threonine (pT), and phospho-tyrosine (pY) sites. DeepPhoPred incorporates a two-headed convolutional neural network architecture with the squeeze and excitation blocks followed by fully connected layers that jointly learn significant features from the peptide's structural and evolutionary information to predict phosphorylation sites. Our empirical results demonstrate that DeepPhoPred significantly outperforms the existing microbial phosphorylation site predictors with its highly efficient deep-learning architecture. DeepPhoPred as a standalone predictor, all its source codes, and our employed datasets are publicly available at https://github.com/faisalahm3d/DeepPhoPred.
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Affiliation(s)
- Faisal Ahmed
- Digital Health Unit, NVISION Systems and Technologies SL, Barcelona, Spain
- Department of Computer Engineering and Mathematics, Universitat Rovira i Virgili, Tarragona, Spain
| | - Alok Sharma
- Laboratory of Medical Science Mathematics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Institute for Integrated and Intelligent Systems, Griffith University, Brisbane, Queensland, Australia
- College of Informatics, Korea University, Seoul, South Korea
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Japan
| | - Swakkhar Shatabda
- Department of Computer Science and Engineering, BRAC University, Dhaka, Bangladesh
| | - Iman Dehzangi
- Department of Computer Science, Rutgers University, Camden, New Jersey, USA
- Center for Computational and Integrative Biology (CCIB), Rutgers University, Camden, New Jersey, USA
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12
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Schofield LC, Dialpuri JS, Murshudov GN, Agirre J. Post-translational modifications in the Protein Data Bank. Acta Crystallogr D Struct Biol 2024; 80:647-660. [PMID: 39207896 PMCID: PMC11394121 DOI: 10.1107/s2059798324007794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024] Open
Abstract
Proteins frequently undergo covalent modification at the post-translational level, which involves the covalent attachment of chemical groups onto amino acids. This can entail the singular or multiple addition of small groups, such as phosphorylation; long-chain modifications, such as glycosylation; small proteins, such as ubiquitination; as well as the interconversion of chemical groups, such as the formation of pyroglutamic acid. These post-translational modifications (PTMs) are essential for the normal functioning of cells, as they can alter the physicochemical properties of amino acids and therefore influence enzymatic activity, protein localization, protein-protein interactions and protein stability. Despite their inherent importance, accurately depicting PTMs in experimental studies of protein structures often poses a challenge. This review highlights the role of PTMs in protein structures, as well as the prevalence of PTMs in the Protein Data Bank, directing the reader to accurately built examples suitable for use as a modelling reference.
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Affiliation(s)
- Lucy C Schofield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Jordan S Dialpuri
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Garib N Murshudov
- MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
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13
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Phillips M, Muthukumar M, Ghosh K. Beyond monopole electrostatics in regulating conformations of intrinsically disordered proteins. PNAS NEXUS 2024; 3:pgae367. [PMID: 39253398 PMCID: PMC11382291 DOI: 10.1093/pnasnexus/pgae367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 08/13/2024] [Indexed: 09/11/2024]
Abstract
Conformations and dynamics of an intrinsically disordered protein (IDP) depend on its composition of charged and uncharged amino acids, and their specific placement in the protein sequence. In general, the charge (positive or negative) on an amino acid residue in the protein is not a fixed quantity. Each of the ionizable groups can exist in an equilibrated distribution of fully ionized state (monopole) and an ion-pair (dipole) state formed between the ionizing group and its counterion from the background electrolyte solution. The dipole formation (counterion condensation) depends on the protein conformation, which in turn depends on the distribution of charges and dipoles on the molecule. Consequently, effective charges of ionizable groups in the IDP backbone may differ from their chemical charges in isolation-a phenomenon termed charge-regulation. Accounting for the inevitable dipolar interactions, that have so far been ignored, and using a self-consistent procedure, we present a theory of charge-regulation as a function of sequence, temperature, and ionic strength. The theory quantitatively agrees with both charge reduction and salt-dependent conformation data of Prothymosin-alpha and makes several testable predictions. We predict charged groups are less ionized in sequences where opposite charges are well mixed compared to sequences where they are strongly segregated. Emergence of dipolar interactions from charge-regulation allows spontaneous coexistence of two phases having different conformations and charge states, sensitively depending on the charge patterning. These findings highlight sequence dependent charge-regulation and its potential exploitation by biological regulators such as phosphorylation and mutations in controlling protein conformation and function.
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Affiliation(s)
- Michael Phillips
- Department of Physics and Astronomy, University of Denver, Denver, CO 80208, USA
| | - Murugappan Muthukumar
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, CO 80208, USA
- Molecular and Cellular Biophysics, University of Denver, Denver, CO 80208, USA
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14
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Trothen S, Teplitsky JE, Armstong RE, Zang RX, Lurie A, Mumby MJ, Edgar CR, Grol MW, Dikeakos JD. PACS-1 Interacts with TRPC3 and ESyt1 to Mediate Protein Trafficking while Promoting SOCE and Cooperatively Regulating Hormone Secretion. ACS OMEGA 2024; 9:35014-35027. [PMID: 39157130 PMCID: PMC11325417 DOI: 10.1021/acsomega.4c04998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 08/20/2024]
Abstract
Corticotropic cells of the anterior pituitary gland release adrenocorticotropic hormone (ACTH) in a regulated manner to promote the production of cortisol and androgens. The process of ACTH secretion is partly mediated by the phosphofurin acidic cluster sorting protein 1 (PACS-1); however, the underlying mechanisms behind this regulation remain unclear. Herein, we demonstrated PACS-1 interactions with the short transient receptor potential channel 3 (TRPC3) calcium transporter and the extended synaptotagmin-1 (ESyt1) endoplasmic reticulum-plasma membrane tethering protein. Importantly, PACS-1 promoted interactions between TRPC3 and ESyt1 and regulated their plasma membrane localization. Lastly, we demonstrated that PACS-1 is required for a proper store-operated calcium entry (SOCE) response and that ESyt1 regulates ACTH secretion through an unknown mechanism regulated by PACS-1. Overall, our study provides new insights into the physiological role PACS-1 plays in modulating intracellular calcium levels and regulating ACTH secretion in corticotropic cells.
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Affiliation(s)
- Steven
M. Trothen
- Department
of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Jack E. Teplitsky
- Department
of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Ryan E. Armstong
- Department
of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Rong Xuan Zang
- Department
of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Antony Lurie
- Department
of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Mitchell J. Mumby
- Department
of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Cassandra R. Edgar
- Department
of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Matthew W. Grol
- Department
of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Jimmy D. Dikeakos
- Department
of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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15
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McIvor JAP, Larsen DS, Mercadante D. Charge Relaying within a Phospho-Motif Rescue Binding Competency of a Disordered Transcription Factor. J Chem Inf Model 2024; 64:6041-6052. [PMID: 39074869 DOI: 10.1021/acs.jcim.4c00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Structural disorder in proteins is central to cellular signaling, where conformational plasticity equips molecules to promiscuously interact with different partners. By engaging with multiple binding partners via the rearrangement of its three helices, the nuclear coactivator binding domain (NCBD) of the CBP/p300 transcription factor is a paradigmatic example of promiscuity. Recently, molecular simulations and experiments revealed that, through the establishment of long-range electrostatic interactions, intended as salt-bridges formed between the post-translationally inserted phosphate and positively charged residues in helix H3 of NCBD, phosphorylation triggers NCBD compaction, lowering its affinity for binding partners. By means of extensive molecular simulations, we here investigated the effect of short-range electrostatics on the conformational ensemble of NCBD, by monitoring the interactions between a phosphorylated serine and conserved positively charged residues within the NCBD phospho-motif. We found that empowering proximal electrostatic interactions, as opposed to long-range electrostatics, can reshape the NCBD ensemble rescuing the binding competency of phosphorylated NCBD. Given the conservation of positive charges in phospho-motifs, proximal electrostatic interactions might dampen the effects of phosphorylation and act as a relay to regulate phosphorylated intrinsically disordered proteins, ultimately tuning the binding affinity for different cellular partners.
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Affiliation(s)
- Jordan A P McIvor
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
| | - Danaé S Larsen
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
| | - Davide Mercadante
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
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16
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Cao X, Ge J, Ma Y, Li H, Han W, Lamont SJ, Sun H. MiR-20a-5p Targeting the TGFBR2 Gene Regulates Inflammatory Response of Chicken Macrophages Infected with Avian Pathogenic E. coli. Animals (Basel) 2024; 14:2277. [PMID: 39123803 PMCID: PMC11311048 DOI: 10.3390/ani14152277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/29/2024] [Accepted: 08/03/2024] [Indexed: 08/12/2024] Open
Abstract
Avian pathogenic E. coli (APEC) causes localized and systemic infections and are a threat to human health. microRNAs (miRNAs) play critical roles in inflammation and immune regulation following pathogen invasion. However, the related regulatory mechanism remains unclear. This study aimed to elucidate the involvement of chicken microRNA-20a-5p (gga-miR-20a-5p) in host defense against APEC in chickens and the underlying mechanisms. We evaluated the expression levels of gga-miR-20a-5p in chicken tissues and cells and observed a significant decrease in expression following APEC infection. Dual luciferase reporter assays showed that gga-miR-20a-5p directly targeted transforming growth factor-beta receptor 2 (TGFBR2), specifically by binding to the 3'-untranslated region (3'UTR) of TGFBR2. Overexpression of gga-miR-20a-5p markedly reduced both the mRNA and protein levels of TGFBR2, whereas inhibition of gga-miR-20a-5p significantly increased expression. Mechanistic investigations revealed that overexpression of gga-miR-20a-5p also attenuated the expression levels of the pro-inflammatory cytokines IL8, TNFα, IL6, and IL1β, whereas inhibition of gga-miR-20a-5p had the opposite effects. Collectively, our findings suggest that gga-miR-20a-5p regulates the immune response during APEC infection by targeting TGFBR2, thereby suppressing inflammatory cytokine production. This study provides valuable insights into the role of gga-miR-20a-5p in the host defense against APEC.
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Affiliation(s)
- Xinqi Cao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jiayi Ge
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yuyi Ma
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Huan Li
- School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou 225009, China
| | - Wei Han
- Jiangsu Institute of Poultry Sciences, Yangzhou 225003, China
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Hongyan Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
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17
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Ghassabi F, Hashempour A, Dehghani B, Hasanshahi Z, Khodadad N, Behizadeh F, Davarpanah MA. Frequency of Fusion Inhibitor Resistance Mutations Among Therapy-Naïve HIV Patients. AIDS Res Hum Retroviruses 2024; 40:471-481. [PMID: 38553905 DOI: 10.1089/aid.2023.0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024] Open
Abstract
Glycoprotein 41 (gp41) of the human immunodeficiency virus type 1 (HIV-1) protein plays a critical role in membrane fusion. Gp41 binds to proteins in the plasma membrane of CD4+ T cells, particularly the T-cell antigen receptor (TCR). These findings indicate that gp41 is involved in the assembly of HIV-1 at the plasma membrane of T cells and affects the stimulation of the TCR. To control HIV-1, new inhibitors were introduced to target the gp41 protein. However, mutations in this region might reduce their efficacy. The Gp41 region was amplified from the sera of 30 patients using nested polymerase chain reaction. The sequences were analyzed by bioinformatics tools to identify mutations and gp41 structural features. Subtyping and the interaction between fusion inhibitors and gp41 proteins were also examined. As the first report from Iran, docking analysis between fusion inhibitors and Iranian gp41 proteins showed that mutations in gp41 could not reduce the efficacy of the fusion inhibitors. Most of the patients were infected with CRF35-AD. Several post-modification positions, including glycosylation and phosphorylation sites, were identified in the gp41 protein. Our findings revealed no known multinational drug resistance to gp41 inhibitors; thus, fusion inhibitors can effectively inhibit HIV in Iranian patients. In addition, the present study introduced a new gp41 region (36-44 aa), which considerably influences the interactions between gp41 inhibitors and the gp41 protein. This region may play a pivotal role in suppressing gp41 inhibitors in CFR35-AD. Furthermore, gp41 can be considered a good target for subtyping analysis via the phylogenetic method.
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Affiliation(s)
- Farzaneh Ghassabi
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ava Hashempour
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Behzad Dehghani
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Hasanshahi
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nastaran Khodadad
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farideh Behizadeh
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohamad Ali Davarpanah
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
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18
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Sondhi Y, Messcher RL, Bellantuono AJ, Storer CG, Cinel SD, Godfrey RK, Mongue AJ, Weng YM, Glass D, St Laurent RA, Hamilton CA, Earl C, Brislawn CJ, Kitching IJ, Bybee SM, Theobald JC, Kawahara AY. Day-night gene expression reveals circadian gene disco as a candidate for diel-niche evolution in moths. Proc Biol Sci 2024; 291:20240591. [PMID: 39194299 DOI: 10.1098/rspb.2024.0591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 08/29/2024] Open
Abstract
Temporal ecological niche partitioning is an underappreciated driver of speciation. While insects have long been models for circadian biology, the genes and circuits that allow adaptive changes in diel-niches remain poorly understood. We compared gene expression in closely related day- and night-active non-model wild silk moths, with otherwise similar ecologies. Using an ortholog-based pipeline to compare RNA-Seq patterns across two moth species, we find over 25 pairs of gene orthologs showing differential expression. Notably, the gene disco, involved in circadian control, optic lobe and clock neuron development in Drosophila, shows robust adult circadian mRNA cycling in moth heads. Disco is highly conserved in moths and has additional zinc-finger domains with specific nocturnal and diurnal mutations. We propose disco as a candidate gene for the diversification of temporal diel-niche in moths.
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Affiliation(s)
- Yash Sondhi
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida , Gainesville, FL 32611, USA
- Department of Biology, Florida International University , Miami, FL 33174, USA
- Institute for Environment, Florida International University , Miami, FL 33174, USA
| | - Rebeccah L Messcher
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida , Gainesville, FL 32611, USA
| | | | - Caroline G Storer
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida , Gainesville, FL 32611, USA
| | - Scott D Cinel
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida , Gainesville, FL 32611, USA
| | - R Keating Godfrey
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida , Gainesville, FL 32611, USA
- Department of Biology, Florida International University , Miami, FL 33174, USA
| | - Andrew J Mongue
- Department of Entomology and Nematology, University of Florida , Gainesville, FL 32611, USA
| | - Yi-Ming Weng
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida , Gainesville, FL 32611, USA
| | - Deborah Glass
- School of Life Sciences, University of Sussex, Sussex House , Brighton BN1 9RH, UK
- Natural History Museum, Cromwell Road , London SW7 5BD, UK
| | - Ryan A St Laurent
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida , Gainesville, FL 32611, USA
- Department of Entomology, Smithsonian Institution, National Museum of Natural History , Washington, DC, USA
| | - Chris A Hamilton
- Department of Entomology, Plant Pathology & Nematology, University of Idaho , Moscow, ID 83844, USA
| | - Chandra Earl
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida , Gainesville, FL 32611, USA
- Biodiversity Knowledge Integration Center, School of Life Sciences, Arizona State University , Tempe, AZ 852281, USA
| | | | - Ian J Kitching
- Natural History Museum, Cromwell Road , London SW7 5BD, UK
| | - Seth M Bybee
- Department of Biology, Monte L. Bean Museum, Brigham Young University, 4102 Life Science Building , Provo, UT 84602, USA
| | - Jamie C Theobald
- Department of Biology, Florida International University , Miami, FL 33174, USA
- Institute for Environment, Florida International University , Miami, FL 33174, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida , Gainesville, FL 32611, USA
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19
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Amjad H, Saleem F, Ahmad M, Nisar U, Arshad Dar H. Comprehensive bioinformatics-based annotation and functional characterization of bovine chymosin protein revealed novel biological insights. FOOD CHEMISTRY. MOLECULAR SCIENCES 2024; 8:100191. [PMID: 38259869 PMCID: PMC10801198 DOI: 10.1016/j.fochms.2023.100191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/23/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024]
Abstract
Chymosin, an aspartic protease present in the stomachs of young ruminants like cows (bovine), causes milk coagulation and cheese production through the breakdown of κ-casein peptide bonds at the Met105-Phe106 site. Bovine chymosin is first synthesized as a pre-prochymosin that is cleaved to produce the mature chymosin protein. Despite significant strides in research, our understanding of this crucial enzyme remains incomplete. The purpose of this work was to perform in silico evolutionary and functional analysis and to gain unique insights into the structure of this protein. For this, the sequence of Bos taurus chymosin from UniProt database was subjected to various bioinformatics analyses. We found that bovine chymosin is a low molecular weight and hydrophilic protein that has homologs in other Bovidae species. Two active sites of aspartic peptidases, along with a functional domain, were identified. Gene Ontology analysis further confirmed chymosin's involvement in proteolysis and aspartic endopeptidase activity. Potential disordered residues and post-translational modification sites were also uncovered. It was revealed that the secondary structure of bovine chymosin is comprised of beta strands (44.27%), coils (43.65%), and alpha helices (12.07%). A highly optimized 3D structure was also obtained. Moreover, crucial protein-protein interactions were unveiled. Altogether, these findings provide valuable insights that could guide future research on bovine chymosin and its biological roles.
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Affiliation(s)
- Hafsa Amjad
- Department of Biotechnology, Lahore College for Women University, Lahore 54590, Pakistan
| | - Faiza Saleem
- Department of Biotechnology, Lahore College for Women University, Lahore 54590, Pakistan
| | - Munir Ahmad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Uzma Nisar
- Department of Biotechnology, Lahore College for Women University, Lahore 54590, Pakistan
| | - Hamza Arshad Dar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad 44000, Pakistan
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20
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Lee YF, Phua CZJ, Yuan J, Zhang B, Lee MY, Kannan S, Chiu YHJ, Koh CWQ, Yap CK, Lim EKH, Chen J, Lim Y, Lee JJH, Skanderup AJ, Wang Z, Zhai W, Tan NS, Verma CS, Tay Y, Tan DSW, Tam WL. PARP4 interacts with hnRNPM to regulate splicing during lung cancer progression. Genome Med 2024; 16:91. [PMID: 39034402 PMCID: PMC11265163 DOI: 10.1186/s13073-024-01328-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/02/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND The identification of cancer driver genes from sequencing data has been crucial in deepening our understanding of tumor biology and expanding targeted therapy options. However, apart from the most commonly altered genes, the mechanisms underlying the contribution of other mutations to cancer acquisition remain understudied. Leveraging on our whole-exome sequencing of the largest Asian lung adenocarcinoma (LUAD) cohort (n = 302), we now functionally assess the mechanistic role of a novel driver, PARP4. METHODS In vitro and in vivo tumorigenicity assays were used to study the functional effects of PARP4 loss and mutation in multiple lung cancer cell lines. Interactomics analysis by quantitative mass spectrometry was conducted to identify PARP4's interaction partners. Transcriptomic data from cell lines and patient tumors were used to investigate splicing alterations. RESULTS PARP4 depletion or mutation (I1039T) promotes the tumorigenicity of KRAS- or EGFR-driven lung cancer cells. Disruption of the vault complex, with which PARP4 is commonly associated, did not alter tumorigenicity, indicating that PARP4's tumor suppressive activity is mediated independently. The splicing regulator hnRNPM is a potentially novel PARP4 interaction partner, the loss of which likewise promotes tumor formation. hnRNPM loss results in splicing perturbations, with a propensity for dysregulated intronic splicing that was similarly observed in PARP4 knockdown cells and in LUAD cohort patients with PARP4 copy number loss. CONCLUSIONS PARP4 is a novel modulator of lung adenocarcinoma, where its tumor suppressive activity is mediated not through the vault complex-unlike conventionally thought, but in association with its novel interaction partner hnRNPM, thus suggesting a role for splicing dysregulation in LUAD tumorigenesis.
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Affiliation(s)
- Yi Fei Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Cheryl Zi Jin Phua
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Ju Yuan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Bin Zhang
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - May Yin Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix, Singapore, 138671, Singapore
| | - Yui Hei Jasper Chiu
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Casslynn Wei Qian Koh
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Choon Kong Yap
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Edwin Kok Hao Lim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Jianbin Chen
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Yuhua Lim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Jane Jia Hui Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Anders Jacobsen Skanderup
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Zhenxun Wang
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
- Centre for Vision Research, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Weiwei Zhai
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Nguan Soon Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Chandra S Verma
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix, Singapore, 138671, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore
| | - Daniel Shao Weng Tan
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.
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21
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Li D, Jia C, Lin G, Dang J, Liu C, Wu Q. Impact of Methyl Jasmonate on Terpenoid Biosynthesis and Functional Analysis of Sesquiterpene Synthesis Genes in Schizonepeta tenuifolia. PLANTS (BASEL, SWITZERLAND) 2024; 13:1920. [PMID: 39065447 PMCID: PMC11280979 DOI: 10.3390/plants13141920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024]
Abstract
This study investigates the impact of methyl jasmonate (MeJA) on the volatile oil composition of Schizonepeta tenuifolia and elucidates the function of the StTPS45 gene, a key player in terpenoid biosynthesis. The effect of different concentrations of MeJA (0, 50, 100, 200, and 300 μmol/L) on the growth of S. tenuifolia adventitious bud clusters was analyzed over a 20 d period. Using gas chromatography-mass spectrometry (GC-MS), 17 compounds were identified from the adventitious bud clusters of S. tenuifolia. Significant changes in the levels of major monoterpenes, including increased contents of (+)-limonene and (+)-menthone, were observed, particularly at higher concentrations of MeJA. Analysis of transcriptome data from three groups treated with 0, 100, and 300 μmol/L MeJA revealed significant changes in the gene expression profiles following MeJA treatment. At 100 μmol/L MeJA, most terpene synthase (TPS) genes were overexpressed. Additionally, gene expression and functional predictions suggested that StTPS45 acts as germacrene D synthase. Therefore, StTPS45 was cloned and expressed in Escherichia coli, and enzyme activity assays confirmed its function as a germacrene D synthase. Molecular docking and structural prediction of StTPS45 further suggested specific interactions with farnesyl diphosphate (FPP), aligning with its role in the terpenoid synthesis pathway. These findings provide valuable insights into the modulation of secondary metabolite pathways by jasmonate signaling and underscore the potential of genetic engineering approaches to enhance the production of specific terpenoids in medicinal plants.
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Affiliation(s)
- Dishuai Li
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.L.); (C.J.); (G.L.); (J.D.)
| | - Congling Jia
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.L.); (C.J.); (G.L.); (J.D.)
| | - Guyin Lin
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.L.); (C.J.); (G.L.); (J.D.)
| | - Jingjie Dang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.L.); (C.J.); (G.L.); (J.D.)
| | - Chanchan Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.L.); (C.J.); (G.L.); (J.D.)
- State Key Laboratory on Technologies for Chinese Medicine Pharmaceutical Process Control and Intelligent Manufacture, Nanjing University of Chinese Medicine, Nanjing 210023, China
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Qinan Wu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.L.); (C.J.); (G.L.); (J.D.)
- State Key Laboratory on Technologies for Chinese Medicine Pharmaceutical Process Control and Intelligent Manufacture, Nanjing University of Chinese Medicine, Nanjing 210023, China
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
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22
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Yogeshwar SM, Muñiz-Castrillo S, Sabater L, Peris-Sempere V, Mallajosyula V, Luo G, Yan H, Yu E, Zhang J, Lin L, Fagundes Bueno F, Ji X, Picard G, Rogemond V, Pinto AL, Heidbreder A, Höftberger R, Graus F, Dalmau J, Santamaria J, Iranzo A, Schreiner B, Giannoccaro MP, Liguori R, Shimohata T, Kimura A, Ono Y, Binks S, Mariotto S, Dinoto A, Bonello M, Hartmann CJ, Tambasco N, Nigro P, Prüss H, McKeon A, Davis MM, Irani SR, Honnorat J, Gaig C, Finke C, Mignot E. HLA-DQB1*05 subtypes and not DRB1*10:01 mediates risk in anti-IgLON5 disease. Brain 2024; 147:2579-2592. [PMID: 38425314 PMCID: PMC11224611 DOI: 10.1093/brain/awae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/09/2023] [Accepted: 01/21/2024] [Indexed: 03/02/2024] Open
Abstract
Anti-IgLON5 disease is a rare and likely underdiagnosed subtype of autoimmune encephalitis. The disease displays a heterogeneous phenotype that includes sleep, movement and bulbar-associated dysfunction. The presence of IgLON5-antibodies in CSF/serum, together with a strong association with HLA-DRB1*10:01∼DQB1*05:01, supports an autoimmune basis. In this study, a multicentric human leukocyte antigen (HLA) study of 87 anti-IgLON5 patients revealed a stronger association with HLA-DQ than HLA-DR. Specifically, we identified a predisposing rank-wise association with HLA-DQA1*01:05∼DQB1*05:01, HLA-DQA1*01:01∼DQB1*05:01 and HLA-DQA1*01:04∼DQB1*05:03 in 85% of patients. HLA sequences and binding cores for these three DQ heterodimers were similar, unlike those of linked DRB1 alleles, supporting a causal link to HLA-DQ. This association was further reflected in an increasingly later age of onset across each genotype group, with a delay of up to 11 years, while HLA-DQ-dosage dependent effects were also suggested by reduced risk in the presence of non-predisposing DQ1 alleles. The functional relevance of the observed HLA-DQ molecules was studied with competition binding assays. These proof-of-concept experiments revealed preferential binding of IgLON5 in a post-translationally modified, but not native, state to all three risk-associated HLA-DQ receptors. Further, a deamidated peptide from the Ig2-domain of IgLON5 activated T cells in two patients, compared with one control carrying HLA-DQA1*01:05∼DQB1*05:01. Taken together, these data support a HLA-DQ-mediated T-cell response to IgLON5 as a potentially key step in the initiation of autoimmunity in this disease.
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Affiliation(s)
- Selina M Yogeshwar
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, 10117, Berlin, Germany
- Einstein Center for Neurosciences Berlin, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Sergio Muñiz-Castrillo
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lidia Sabater
- Neuroimmunology Program, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer, Caixa Research Institute, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Vicente Peris-Sempere
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Guo Luo
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Han Yan
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eric Yu
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jing Zhang
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ling Lin
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Flavia Fagundes Bueno
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xuhuai Ji
- Human Immune Monitoring Center, Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Géraldine Picard
- French Reference Center on Paraneoplastic Neurological Syndrome and Autoimmune Encephalitis, Hospices Civils de Lyon, 69677, Lyon, France
- Institut MeLiS INSERM U1314/CNRS UMR 5284, Université Claude Bernard Lyon 1, 69372 Lyon, France
| | - Véronique Rogemond
- French Reference Center on Paraneoplastic Neurological Syndrome and Autoimmune Encephalitis, Hospices Civils de Lyon, 69677, Lyon, France
- Institut MeLiS INSERM U1314/CNRS UMR 5284, Université Claude Bernard Lyon 1, 69372 Lyon, France
| | - Anne Laurie Pinto
- French Reference Center on Paraneoplastic Neurological Syndrome and Autoimmune Encephalitis, Hospices Civils de Lyon, 69677, Lyon, France
- Institut MeLiS INSERM U1314/CNRS UMR 5284, Université Claude Bernard Lyon 1, 69372 Lyon, France
| | - Anna Heidbreder
- Kepler University Hospital, Department of Neurology, Johannes Kepler University, 4020 Linz, Austria
| | - Romana Höftberger
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
| | - Francesc Graus
- Neurology Service, Hospital Clínic of Barcelona, Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Josep Dalmau
- Neurology Service, Hospital Clínic of Barcelona, Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Spanish National Network for Research on Rare Diseases (CIBERER), 28029 Madrid, Spain
| | - Joan Santamaria
- Neurology Service, Hospital Clínic of Barcelona, Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Alex Iranzo
- Neurology Service, Hospital Clínic of Barcelona, Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Bettina Schreiner
- Department of Neurology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Experimental Immunology, University of Zurich, 8057 Zurich, Switzerland
| | - Maria Pia Giannoccaro
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, 40139 Bologna, Italy
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, 40100 Bologna, Italy
| | - Rocco Liguori
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, 40139 Bologna, Italy
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, 40100 Bologna, Italy
| | - Takayoshi Shimohata
- Department of Neurology, Gifu University Graduate School of Medicine, 501-1194 Gifu, Japan
| | - Akio Kimura
- Department of Neurology, Gifu University Graduate School of Medicine, 501-1194 Gifu, Japan
| | - Yoya Ono
- Department of Neurology, Gifu University Graduate School of Medicine, 501-1194 Gifu, Japan
| | - Sophie Binks
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
- Department of Neurology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Sara Mariotto
- Neurology Unit, Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, 37124 Verona, Italy
| | - Alessandro Dinoto
- Neurology Unit, Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, 37124 Verona, Italy
| | - Michael Bonello
- Department of Neurology, The Walton Centre NHS Foundation Trust, L9 7LJ, Liverpool, UK
| | - Christian J Hartmann
- Department of Neurology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Nicola Tambasco
- Movement Disorders Center, Neurology Department, Perugia General Hospital and University of Perugia, 06156 Perugia, Italy
| | - Pasquale Nigro
- Movement Disorders Center, Neurology Department, Perugia General Hospital and University of Perugia, 06156 Perugia, Italy
| | - Harald Prüss
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, 10117, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany
| | - Andrew McKeon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarosh R Irani
- Department of Neurology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Jérôme Honnorat
- French Reference Center on Paraneoplastic Neurological Syndrome and Autoimmune Encephalitis, Hospices Civils de Lyon, 69677, Lyon, France
- Institut MeLiS INSERM U1314/CNRS UMR 5284, Université Claude Bernard Lyon 1, 69372 Lyon, France
| | - Carles Gaig
- Neurology Service, Hospital Clínic of Barcelona, Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Carsten Finke
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, 10117, Berlin, Germany
- Berlin Center for Advanced Neuroimaging, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Emmanuel Mignot
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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23
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Matheny CJ, Qadota H, Bailey AO, Valdebenito-Silva S, Oberhauser AF, Benian GM. The myosin chaperone UNC-45 has an important role in maintaining the structure and function of muscle sarcomeres during adult aging. Mol Biol Cell 2024; 35:ar98. [PMID: 38809582 PMCID: PMC11244168 DOI: 10.1091/mbc.e23-12-0488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/26/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024] Open
Abstract
C. elegans undergo age-dependent declines in muscle organization and function, similar to human sarcopenia. The chaperone UNC-45 is required to fold myosin heads after translation and is likely used for refolding after thermally- or chemically-induced unfolding. UNC-45's TPR region binds HSP-90 and its UCS domain binds myosin heads. We observe early onset sarcopenia when UNC-45 is reduced at the beginning of adulthood. There is sequential decline of HSP-90, UNC-45, and MHC B myosin. A mutation in age-1 delays sarcopenia and loss of HSP-90, UNC-45, and myosin. UNC-45 undergoes age-dependent phosphorylation, and mass spectrometry reveals phosphorylation of six serines and two threonines, seven of which occur in the UCS domain. Additional expression of UNC-45 results in maintenance of MHC B myosin and suppression of A-band disorganization in old animals. Our results suggest that increased expression or activity of UNC-45 might be a strategy for prevention or treatment of sarcopenia.
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Affiliation(s)
| | - Hiroshi Qadota
- Department of Pathology, Emory University, Atlanta, GA 30322
| | - Aaron O. Bailey
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550
| | | | - Andres F. Oberhauser
- Department of Neurobiology, University of Texas Medical Branch, Galveston, TX 77550
| | - Guy M. Benian
- Department of Pathology, Emory University, Atlanta, GA 30322
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24
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Yu Z, Yu J, Wang H, Zhang S, Zhao L, Shi S. PhosAF: An integrated deep learning architecture for predicting protein phosphorylation sites with AlphaFold2 predicted structures. Anal Biochem 2024; 690:115510. [PMID: 38513769 DOI: 10.1016/j.ab.2024.115510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
Phosphorylation is indispensable in comprehending biological processes, while biological experimental methods for identifying phosphorylation sites are tedious and arduous. With the rapid growth of biotechnology, deep learning methods have made significant progress in site prediction tasks. Nevertheless, most existing predictors only consider protein sequence information, that limits the capture of protein spatial information. Building upon the latest advancement in protein structure prediction by AlphaFold2, a novel integrated deep learning architecture PhosAF is developed to predict phosphorylation sites in human proteins by integrating CMA-Net and MFC-Net, which considers sequence and structure information predicted by AlphaFold2. Here, CMA-Net module is composed of multiple convolutional neural network layers and multi-head attention is appended to obtaining the local and long-term dependencies of sequence features. Meanwhile, the MFC-Net module composed of deep neural network layers is used to capture the complex representations of evolutionary and structure features. Furthermore, different features are combined to predict the final phosphorylation sites. In addition, we put forward a new strategy to construct reliable negative samples via protein secondary structures. Experimental results on independent test data and case study indicate that our model PhosAF surpasses the current most advanced methods in phosphorylation site prediction.
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Affiliation(s)
- Ziyuan Yu
- Department of Mathematics, School of Mathematics and Computer Sciences, Nanchang University, Nanchang, 330031, China.
| | - Jialin Yu
- Department of Mathematics, School of Mathematics and Computer Sciences, Nanchang University, Nanchang, 330031, China.
| | - Hongmei Wang
- Department of Mathematics, School of Mathematics and Computer Sciences, Nanchang University, Nanchang, 330031, China.
| | - Shuai Zhang
- Department of Mathematics, School of Mathematics and Computer Sciences, Nanchang University, Nanchang, 330031, China.
| | - Long Zhao
- Department of Mathematics, School of Mathematics and Computer Sciences, Nanchang University, Nanchang, 330031, China.
| | - Shaoping Shi
- Department of Mathematics, School of Mathematics and Computer Sciences, Nanchang University, Nanchang, 330031, China; Institute of Mathematics and Interdisciplinary Sciences, Nanchang University, Nanchang, 330031, China.
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25
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Lim CP, Leow CH, Lim HT, Kok BH, Chuah C, Oliveira JIN, Jones M, Leow CY. Insights into structural vaccinology harnessed for universal coronavirus vaccine development. Clin Exp Vaccine Res 2024; 13:202-217. [PMID: 39144127 PMCID: PMC11319108 DOI: 10.7774/cevr.2024.13.3.202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 08/16/2024] Open
Abstract
Structural vaccinology is pivotal in expediting vaccine design through high-throughput screening of immunogenic antigens. Leveraging the structural and functional characteristics of antigens and immune cell receptors, this approach employs protein structural comparison to identify conserved patterns in key pathogenic components. Molecular modeling techniques, including homology modeling and molecular docking, analyze specific three-dimensional (3D) structures and protein interactions and offer valuable insights into the 3D interactions and binding affinity between vaccine candidates and target proteins. In this review, we delve into the utilization of various immunoinformatics and molecular modeling tools to streamline the development of broad-protective vaccines against coronavirus disease 2019 variants. Structural vaccinology significantly enhances our understanding of molecular interactions between hosts and pathogens. By accelerating the pace of developing effective and targeted vaccines, particularly against the rapidly mutating severe acute respiratory syndrome coronavirus 2 and other prevalent infectious diseases, this approach stands at the forefront of advancing immunization strategies. The combination of computational techniques and structural insights not only facilitates the identification of potential vaccine candidates but also contributes to the rational design of vaccines, fostering a more efficient and targeted approach to combatting infectious diseases.
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Affiliation(s)
- Chin Peng Lim
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor, Malaysia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor, Malaysia
| | - Hui Ting Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor, Malaysia
| | - Boon Hui Kok
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor, Malaysia
| | - Candy Chuah
- Faculty of Medicine, Asian Institute of Medical Science and Technology University, Bedong, Malaysia
| | - Jonas Ivan Nobre Oliveira
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Malcolm Jones
- School of Veterinary Science, The University of Queensland, Gatton, Australia
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia
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Ng NHJ, Ghosh S, Bok CM, Ching C, Low BSJ, Chen JT, Lim E, Miserendino MC, Tan YS, Hoon S, Teo AKK. HNF4A and HNF1A exhibit tissue specific target gene regulation in pancreatic beta cells and hepatocytes. Nat Commun 2024; 15:4288. [PMID: 38909044 PMCID: PMC11193738 DOI: 10.1038/s41467-024-48647-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/08/2024] [Indexed: 06/24/2024] Open
Abstract
HNF4A and HNF1A encode transcription factors that are important for the development and function of the pancreas and liver. Mutations in both genes have been directly linked to Maturity Onset Diabetes of the Young (MODY) and type 2 diabetes (T2D) risk. To better define the pleiotropic gene regulatory roles of HNF4A and HNF1A, we generated a comprehensive genome-wide map of their binding targets in pancreatic and hepatic cells using ChIP-Seq. HNF4A was found to bind and regulate known (ACY3, HAAO, HNF1A, MAP3K11) and previously unidentified (ABCD3, CDKN2AIP, USH1C, VIL1) loci in a tissue-dependent manner. Functional follow-up highlighted a potential role for HAAO and USH1C as regulators of beta cell function. Unlike the loss-of-function HNF4A/MODY1 variant I271fs, the T2D-associated HNF4A variant (rs1800961) was found to activate AKAP1, GAD2 and HOPX gene expression, potentially due to changes in DNA-binding affinity. We also found HNF1A to bind to and regulate GPR39 expression in beta cells. Overall, our studies provide a rich resource for uncovering downstream molecular targets of HNF4A and HNF1A that may contribute to beta cell or hepatic cell (dys)function, and set up a framework for gene discovery and functional validation.
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Affiliation(s)
- Natasha Hui Jin Ng
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Soumita Ghosh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Chek Mei Bok
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Carmen Ching
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Blaise Su Jun Low
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Juin Ting Chen
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore
| | - Euodia Lim
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore
| | - María Clara Miserendino
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina
- Bioinformatics Institute, A*STAR, Singapore, 138671, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute, A*STAR, Singapore, 138671, Singapore
| | - Shawn Hoon
- Molecular Engineering Laboratory, IMCB, A*STAR, Singapore, 138673, Singapore
| | - Adrian Kee Keong Teo
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.
- Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore.
- Precision Medicine Translational Research Programme (TRP), National University of Singapore, Singapore, 119228, Singapore.
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27
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Shahidi P, Bahramnejad B, Vafaee Y, Dastan D, Heidari P. Isolation and Characterization of Phenylalanine Ammonia Lyase ( PAL) Genes in Ferula pseudalliacea: Insights into the Phenylpropanoid Pathway. Genes (Basel) 2024; 15:771. [PMID: 38927707 PMCID: PMC11203166 DOI: 10.3390/genes15060771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Phenylalanine ammonia lyase (PAL) is a key enzyme regulating the biosynthesis of the compounds of the phenylpropanoid pathway. This study aimed to isolate and characterize PAL genes from Ferula pseudalliacea Rech.f. (Apiales: Apiaceae) to better understand the regulation of metabolite production. Three PAL gene isoforms (FpPAL1-3) were identified and cloned using the 3'-RACE technique and confirmed by sequencing. Bioinformatics analysis revealed important structural features, such as phosphorylation sites, physicochemical properties, and evolutionary relationships. Expression analysis by qPCR demonstrated the differential transcription profiles of each FpPAL isoform across roots, stems, leaves, flowers, and seeds. FpPAL1 showed the highest expression in stems, FpPAL2 in roots and flowers, and FpPAL3 in flowers. The presence of three isoforms of PAL in F. pseudalliacea, along with the diversity of PAL genes and their tissue-specific expression profiles, suggests that complex modes of regulation exist for phenylpropanoid biosynthesis in this important medicinal plant. The predicted interaction network revealed associations with key metabolic pathways, emphasizing the multifaceted roles of these PAL genes. In silico biochemical analyses revealed the hydrophilicity of the FpPAL isozyme; however, further analysis of substrate specificity and enzyme kinetics can clarify the specific role of each FpPAL isozyme. These comprehensive results increase the understanding of PAL genes in F. pseudalliacea, helping to characterize their contributions to secondary metabolite biosynthesis.
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Affiliation(s)
- Pegah Shahidi
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, Sanandaj 6617715175, Iran;
| | - Bahman Bahramnejad
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, Sanandaj 6617715175, Iran;
| | - Yavar Vafaee
- Department of Horticultural Sciences, Faculty of Agriculture, University of Kurdistan, Sanandaj 6617715175, Iran;
| | - Dara Dastan
- Department of Pharmacognosy, School of Pharmacy, Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan 6517838736, Iran;
| | - Parviz Heidari
- Faculty of Agriculture, Shahrood University of Technology, Shahrood 3619995161, Iran
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28
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Subhadarshini S, Tandon H, Srinivasan N, Sowdhamini R. Normal Mode Analysis Elicits Conformational Shifts in Proteins at Both Proximal and Distal Regions to the Phosphosite Stemming from Single-Site Phosphorylation. ACS OMEGA 2024; 9:24520-24537. [PMID: 38882086 PMCID: PMC11170700 DOI: 10.1021/acsomega.4c00523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/29/2024] [Accepted: 05/13/2024] [Indexed: 06/18/2024]
Abstract
Phosphorylation, a fundamental biochemical switch, intricately regulates protein function and signaling pathways. Our study employs extensive computational structural analyses on a curated data set of phosphorylated and unphosphorylated protein pairs to explore the multifaceted impact of phosphorylation on protein conformation. Using normal mode analysis (NMA), we investigated changes in protein flexibility post-phosphorylation, highlighting an enhanced level of structural dynamism. Our findings reveal that phosphorylation induces not only local changes at the phosphorylation site but also extensive alterations in distant regions, showcasing its far-reaching influence on protein structure-dynamics. Through in-depth case studies on polyubiquitin B and glycogen synthase kinase-3 beta, we elucidate how phosphorylation at distinct sites leads to variable structural and dynamic modifications, potentially dictating functional outcomes. While phosphorylation largely preserves the residue motion correlation, it significantly disrupts low-frequency global modes, presenting a dualistic impact on protein dynamics. We also explored alterations in the total accessible surface area (ASA), emphasizing region-specific changes around phosphorylation sites. This study sheds light on phosphorylation-induced conformational changes, dynamic modulation, and surface accessibility alterations, leveraging an integrated computational approach with RMSD, NMA, and ASA, thereby contributing to a comprehensive understanding of cellular regulation and suggesting promising avenues for therapeutic interventions.
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Affiliation(s)
| | - Himani Tandon
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - Ramanathan Sowdhamini
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
- Computational Approaches to Protein Science, National Centre for Biological Sciences, Bangalore 560065, India
- Computational Biology, Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India
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29
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Mahur P, Sharma A, Jahan G, S G A, Kumar Singh A, Muthukumaran J, Jain M. Understanding Genetic Risks: Computational Exploration of Human β-Synuclein nsSNPs and their Potential Impact on Structural Alteration. Neurosci Lett 2024; 833:137826. [PMID: 38768940 DOI: 10.1016/j.neulet.2024.137826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Synucleins are pivotal in neurodegenerative conditions. Beta-synuclein (β-synuclein) is part of the synuclein protein family alongside alpha-synuclein (α-synuclein) and gamma-synuclein (γ-synuclein). These proteins, found mainly in brain tissue and cancers, are soluble and unstructured. β-synuclein shares significant similarity with α-synuclein, especially in their N-terminus, with a 90% match. However, their aggregation tendencies differ significantly. While α-synuclein aggregation is believed to be counteracted by β-synuclein, which occurs in conditions like Parkinson's disease, β-synuclein may counteract α-synuclein's toxic effects on the nervous system, offering potential treatment for neurodegenerative diseases. Under normal circumstances, β-synuclein may guard against disease by interacting with α-synuclein. Yet, in pathological environments with heightened levels or toxic substances, it might contribute to disease. Our research aims to explore potential harmful mutations in the β-synuclein using computational tools to predict their destabilizing impact on protein structure. Consensus analysis revealed rs1207608813 (A63P), rs1340051870 (S72F), and rs1581178262 (G36C) as deleterious. These findings highlight the intricate relationship between nsSNPs and protein function, shedding light on their potential implications in disease pathways. Understanding the structural consequences of nsSNPs is crucial for elucidating their role in pathogenesis and developing targeted therapeutic interventions. Our results offer a robust computational framework for identifying neurodegenerative disorder-related mutations from SNP datasets, potentially reducing the costs associated with experimental characterization.
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Affiliation(s)
- Pragati Mahur
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Abhishek Sharma
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Gulnaz Jahan
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Adithya S G
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Amit Kumar Singh
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India.
| | - Monika Jain
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India.
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30
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Fló M, Pellizza L, Durán R, Alvarez B, Fernández C. The monodomain Kunitz protein EgKU-7 from the dog tapeworm Echinococcus granulosus is a high-affinity trypsin inhibitor with two interaction sites. Biochem J 2024; 481:717-739. [PMID: 38752933 DOI: 10.1042/bcj20230514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 06/01/2024]
Abstract
Typical Kunitz proteins (I2 family of the MEROPS database, Kunitz-A family) are metazoan competitive inhibitors of serine peptidases that form tight complexes of 1:1 stoichiometry, mimicking substrates. The cestode Echinococcus granulosus, the dog tapeworm causing cystic echinococcosis in humans and livestock, encodes an expanded family of monodomain Kunitz proteins, some of which are secreted to the dog host interface. The Kunitz protein EgKU-7 contains, in addition to the Kunitz domain with the anti-peptidase loop comprising a critical arginine, a C-terminal extension of ∼20 amino acids. Kinetic, electrophoretic, and mass spectrometry studies using EgKU-7, a C-terminally truncated variant, and a mutant in which the critical arginine was substituted by alanine, show that EgKU-7 is a tight inhibitor of bovine and canine trypsins with the unusual property of possessing two instead of one site of interaction with the peptidases. One site resides in the anti-peptidase loop and is partially hydrolyzed by bovine but not canine trypsins, suggesting specificity for the target enzymes. The other site is located in the C-terminal extension. This extension can be hydrolyzed in a particular arginine by cationic bovine and canine trypsins but not by anionic canine trypsin. This is the first time to our knowledge that a monodomain Kunitz-A protein is reported to have two interaction sites with its target. Considering that putative orthologs of EgKU-7 are present in other cestodes, our finding unveils a novel piece in the repertoire of peptidase-inhibitor interactions and adds new notes to the evolutionary host-parasite concerto.
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Affiliation(s)
- Martín Fló
- Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Leonardo Pellizza
- Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Rosario Durán
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo and Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Cecilia Fernández
- Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
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31
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Li T, Wang Y, Natran A, Zhang Y, Wang H, Du K, Qin P, Yuan H, Chen W, Tu B, Inzé D, Dubois M. C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 contributes to GA-mediated growth and flowering by interaction with DELLA proteins. THE NEW PHYTOLOGIST 2024; 242:2555-2569. [PMID: 38594216 DOI: 10.1111/nph.19742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/14/2024] [Indexed: 04/11/2024]
Abstract
Gibberellic acid (GA) plays a central role in many plant developmental processes and is crucial for crop improvement. DELLA proteins, the core suppressors in the GA signaling pathway, are degraded by GA via the 26S proteasomal pathway to release the GA response. However, little is known about the phosphorylation-mediated regulation of DELLA proteins. In this study, we combined GA response assays with protein-protein interaction analysis to infer the connection between Arabidopsis thaliana DELLAs and the C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 (CPL3), a phosphatase involved in the dephosphorylation of RNA polymerase II. We show that CPL3 directly interacts with DELLA proteins and promotes DELLA protein stability by inhibiting its degradation by the 26S proteasome. Consequently, CPL3 negatively modulates multiple GA-mediated processes of plant development, including hypocotyl elongation, flowering time, and anthocyanin accumulation. Taken together, our findings demonstrate that CPL3 serves as a novel regulator that could improve DELLA stability and thereby participate in GA signaling transduction.
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Affiliation(s)
- Ting Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, 611130, Chengdu, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Gent, Belgium
| | - Yongqin Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, 611130, Chengdu, China
| | - Annelore Natran
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Gent, Belgium
| | - Yi Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, 611130, Chengdu, China
| | - Hao Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Kangxi Du
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Peng Qin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Hua Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, 611130, Chengdu, China
| | - Weilan Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Bin Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Gent, Belgium
| | - Marieke Dubois
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Gent, Belgium
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32
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Zhuang C, Yang S, Gonzalez CG, Ainsworth RI, Li S, Kobayashi MT, Wierzbicki I, Rossitto LAM, Wen Y, Peti W, Stanford SM, Gonzalez DJ, Murali R, Santelli E, Bottini N. A novel gain-of-function phosphorylation site modulates PTPN22 inhibition of TCR signaling. J Biol Chem 2024; 300:107393. [PMID: 38777143 PMCID: PMC11237943 DOI: 10.1016/j.jbc.2024.107393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/20/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Protein tyrosine phosphatase nonreceptor type 22 (PTPN22) is encoded by a major autoimmunity gene and is a known inhibitor of T cell receptor (TCR) signaling and drug target for cancer immunotherapy. However, little is known about PTPN22 posttranslational regulation. Here, we characterize a phosphorylation site at Ser325 situated C terminal to the catalytic domain of PTPN22 and its roles in altering protein function. In human T cells, Ser325 is phosphorylated by glycogen synthase kinase-3 (GSK3) following TCR stimulation, which promotes its TCR-inhibitory activity. Signaling through the major TCR-dependent pathway under PTPN22 control was enhanced by CRISPR/Cas9-mediated suppression of Ser325 phosphorylation and inhibited by mimicking it via glutamic acid substitution. Global phospho-mass spectrometry showed Ser325 phosphorylation state alters downstream transcriptional activity through enrichment of Swi3p, Rsc8p, and Moira domain binding proteins, and next-generation sequencing revealed it differentially regulates the expression of chemokines and T cell activation pathways. Moreover, in vitro kinetic data suggest the modulation of activity depends on a cellular context. Finally, we begin to address the structural and mechanistic basis for the influence of Ser325 phosphorylation on the protein's properties by deuterium exchange mass spectrometry and NMR spectroscopy. In conclusion, this study explores the function of a novel phosphorylation site of PTPN22 that is involved in complex regulation of TCR signaling and provides details that might inform the future development of allosteric modulators of PTPN22.
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Affiliation(s)
- Chuling Zhuang
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA
| | - Shen Yang
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA; Department of Medicine, Kao Autoimmunity Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Carlos G Gonzalez
- Department of Pharmacology, University of California, San Diego, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA
| | - Richard I Ainsworth
- Department of Medicine, Kao Autoimmunity Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Sheng Li
- Department of Medicine, University of California, San Diego, California, USA
| | - Masumi Takayama Kobayashi
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, Connecticut, USA
| | - Igor Wierzbicki
- Department of Pharmacology, University of California, San Diego, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA
| | - Leigh-Ana M Rossitto
- Department of Pharmacology, University of California, San Diego, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA
| | - Yutao Wen
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA
| | - Wolfgang Peti
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, Connecticut, USA
| | - Stephanie M Stanford
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Eugenio Santelli
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA; Department of Medicine, Kao Autoimmunity Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Nunzio Bottini
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA; Department of Medicine, Kao Autoimmunity Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA.
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33
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Divya D, Robin AHK, Cho LH, Kim D, Lee DJ, Kim CK, Chung MY. Genome-wide characterization and expression profiling of E2F/DP gene family members in response to abiotic stress in tomato (Solanum lycopersicum L.). BMC PLANT BIOLOGY 2024; 24:436. [PMID: 38773361 PMCID: PMC11110339 DOI: 10.1186/s12870-024-05107-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 05/05/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND E2F/DP (Eukaryotic 2 transcription factor/dimerization partner) family proteins play an essential function in the cell cycle development of higher organisms. E2F/DP family genes have been reported only in a few plant species. However, comprehensive genome-wide characterization analysis of the E2F/DP gene family of Solanum lycopersicum has not been reported so far. RESULTS This study identified eight nonredundant SlE2F/DP genes that were classified into seven groups in the phylogenetic analysis. All eight genes had a single E2F-TDP domain and few genes had additional domains. Two segmental duplication gene pairs were observed within tomato, in addition to cis-regulatory elements, miRNA target sites and phosphorylation sites which play an important role in plant development and stress response in tomato. To explore the three-dimensional (3D) models and gene ontology (GO) annotations of SlE2F/DP proteins, we pointed to their putative transporter activity and their interaction with several putative ligands. The localization of SlE2F/DP-GFP fused proteins in the nucleus and endoplasmic reticulum suggested that they may act in other biological functions. Expression studies revealed the differential expression pattern of most of the SlE2F/DP genes in various organs. Moreover, the expression of E2F/DP genes against abiotic stress, particularly SlE2F/DP2 and/or SlE2F/DP7, was upregulated in response to heat, salt, cold and ABA treatment. Furthermore, the co-expression analysis of SlE2F/DP genes with multiple metabolic pathways was co-expressed with defence genes, transcription factors and so on, suggested their crucial role in various biological processes. CONCLUSIONS Overall, our findings provide a way to understand the structure and function of SlE2F/DP genes; it might be helpful to improve fruit development and tolerance against abiotic stress through marker-assisted selection or transgenic approaches.
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Affiliation(s)
- Dhanasekar Divya
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea
| | - Arif Hasan Khan Robin
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Lae-Hyeon Cho
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang-si, Gyeongsangnam-do, 50463, Republic of Korea
| | - Dohyeon Kim
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang-si, Gyeongsangnam-do, 50463, Republic of Korea
| | - Do-Jin Lee
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea
| | - Chang-Kil Kim
- Department of Horticulture, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Mi-Young Chung
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea.
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Arendt-Tranholm A, Mwirigi JM, Price TJ. RNA isoform expression landscape of the human dorsal root ganglion generated from long-read sequencing. Pain 2024:00006396-990000000-00606. [PMID: 38809314 DOI: 10.1097/j.pain.0000000000003255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/14/2024] [Indexed: 05/30/2024]
Abstract
ABSTRACT Splicing is a posttranscriptional RNA processing mechanism that enhances genomic complexity by creating multiple isoforms from the same gene. We aimed to characterize the isoforms expressed in the human peripheral nervous system, with the goal of creating a resource to identify novel isoforms of functionally relevant genes associated with somatosensation and nociception. We used long-read sequencing to document isoform expression in the human dorsal root ganglia from 3 organ donors and validated in silico by confirming expression in short-read sequencing from 3 independent organ donors. Nineteen thousand five hundred forty-seven isoforms of protein-coding genes were detected and validated. We identified 763 isoforms with at least one previously undescribed splice junction. Previously unannotated isoforms of multiple pain-associated genes, including ASIC3, MRGPRX1, and HNRNPK, were identified. In the novel isoforms of ASIC3, a region comprising approximately 35% of the 5'UTR was excised. By contrast, a novel splice junction was used in isoforms of MRGPRX1 to include an additional exon upstream of the start codon, consequently adding a region to the 5'UTR. Novel isoforms of HNRNPK were identified, which used previously unannotated splice sites to both excise exon 14 and include a sequence in the 3' end of exon 13. This novel insertion is predicted to introduce a tyrosine phosphorylation site potentially phosphorylated by SRC. We also independently confirm a recently reported DRG-specific splicing event in WNK1 that gives insight into how painless peripheral neuropathy occurs when this gene is mutated. Our findings give a clear overview of mRNA isoform diversity in the human dorsal root ganglia obtained using long-read sequencing.
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Affiliation(s)
- Asta Arendt-Tranholm
- Department of Neuroscience and Center for Advanced Pain Studies, School of Behavioral and Brain Sciences, The University of Texas at Dallas, Richardson, TX, United States
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Mortazavi B, Molaei A, Fard NA. Multi-epitopevaccines, from design to expression; an in silico approach. Hum Immunol 2024; 85:110804. [PMID: 38658216 DOI: 10.1016/j.humimm.2024.110804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/02/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
The development of vaccines against a wide range of infectious diseases and pathogens often relies on multi-epitope strategies that can effectively stimulate both humoral and cellular immunity. Immunoinformatics tools play a pivotal role in designing such vaccines, enhancing immune response potential, and minimizing the risk of failure. This review presents a comprehensive overview of practical tools for epitope prediction and the associated immune responses. These immunoinformatics tools facilitate the selection of epitopes based on parameters such as antigenicity, absence of toxic and allergenic sequences, secondary and tertiary structures, sequence conservation, and population coverage. The chosen epitopes can be tailored for B-cells or T-cells, both of which require further assessments covered in this study. We offer a range of suitable linkers that effectively separate cytotoxic T lymphocyte and helper T lymphocyte epitopes while preserving their functionality. Additionally, we identify various adjuvants for specific purposes. We delve into the evaluation of MHC-epitope interactions, MHC clusters, and the simulation of final constructs through molecular docking techniques. We provide diverse linkers and adjuvants optimized for epitope functions to bolster immune responses through epitope attachment. By leveraging these comprehensive tools, the development of multi-epitope vaccines holds the promise of robust immunity and a significant reduction in experimental costs.
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Affiliation(s)
- Behnam Mortazavi
- Department of systems Biotechnology, Faculty of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Ali Molaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Najaf Allahyari Fard
- Department of systems Biotechnology, Faculty of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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Rueda-García V, Rondón-Barragán IS. Molecular Characterization of Neurogranin (NRGN) Gene from Red‑Bellied Pacu (Piaractus brachypomus). Mol Neurobiol 2024; 61:2620-2630. [PMID: 37922064 PMCID: PMC11043121 DOI: 10.1007/s12035-023-03700-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/06/2023] [Indexed: 11/05/2023]
Abstract
Neurogranin (NRGN) is a small brain protein expressed in various telencephalic areas and plays an essential role in synaptic plasticity by regulating the availability of calmodulin (CaM). The study aims to characterize the neurogranin gene in Colombian native fish, red-bellied pacu, Piaractus brachypomus, its basal tissue expression and differential expression in brain injury and sublethal toxicity by organophosphates. NRGN gene contains an open reading frame of 183 nucleotides encoding for 60 amino acids. Bioinformatics analysis showed an IQ motif necessary in the interaction with CaM. NRGN mRNA was detected in tissues with higher expression in brain, gills, and head kidney. In brain regions, NRGN showed high expression in the telencephalon (TE) and olfactory bulb (OB). In the sublethal toxicity experiment, NRGN mRNA was upregulated in individuals under organophosphate exposure in the OB and optic chiasm (OC). In brain injury experiment, NRGN showed upregulation at 14 days in OC and at 24 h and 7 days in TE. These findings demonstrate the differential expression of NRGN under different experimental conditions which make it a candidate for a biomarker in the brain of P. brachypomus.
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Affiliation(s)
- Valentina Rueda-García
- Research Group in Immunobiology and Pathogenesis, Laboratory of Immunology and Molecular Biology, Faculty of Veterinary Medicine and Zootechnics, Universidad del Tolima, Building 33 L105, 730002, Ibagué, Tolima, Colombia
| | - Iang Schroniltgen Rondón-Barragán
- Research Group in Immunobiology and Pathogenesis, Laboratory of Immunology and Molecular Biology, Faculty of Veterinary Medicine and Zootechnics, Universidad del Tolima, Building 33 L105, 730002, Ibagué, Tolima, Colombia.
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Liu L, Lei I, Tian S, Gao W, Guo Y, Li Z, Sabry Z, Tang P, Chen YE, Wang Z. 14-3-3 binding motif phosphorylation disrupts Hdac4-organized condensates to stimulate cardiac reprogramming. Cell Rep 2024; 43:114054. [PMID: 38578832 PMCID: PMC11081035 DOI: 10.1016/j.celrep.2024.114054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 01/15/2024] [Accepted: 03/20/2024] [Indexed: 04/07/2024] Open
Abstract
Cell fate conversion is associated with extensive post-translational modifications (PTMs) and architectural changes of sub-organelles, yet how these events are interconnected remains unknown. We report here the identification of a phosphorylation code in 14-3-3 binding motifs (PC14-3-3) that greatly stimulates induced cardiomyocyte (iCM) formation from fibroblasts. PC14-3-3 is identified in pivotal functional proteins for iCM reprogramming, including transcription factors and chromatin modifiers. Akt1 kinase and protein phosphatase 2A are the key writer and key eraser of the PC14-3-3 code, respectively. PC14-3-3 activation induces iCM formation with the presence of only Tbx5. In contrast, PC14-3-3 inhibition by mutagenesis or inhibitor-mediated code removal abolishes reprogramming. We discover that key PC14-3-3-embedded factors, such as histone deacetylase 4 (Hdac4), Mef2c, and Foxo1, form Hdac4-organized inhibitory nuclear condensates. PC14-3-3 activation disrupts Hdac4 condensates to promote cardiac gene expression. Our study suggests that sub-organelle dynamics regulated by a PTM code could be a general mechanism for stimulating cell reprogramming.
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Affiliation(s)
- Liu Liu
- Department of Cardiac Surgery, Frankel Cardiovascular Center, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Ienglam Lei
- Department of Cardiac Surgery, Frankel Cardiovascular Center, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Shuo Tian
- Department of Cardiac Surgery, Frankel Cardiovascular Center, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Wenbin Gao
- Department of Cardiac Surgery, Frankel Cardiovascular Center, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Yijing Guo
- Department of Cardiac Surgery, Frankel Cardiovascular Center, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhaokai Li
- Department of Cardiac Surgery, Frankel Cardiovascular Center, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Ziad Sabry
- Department of Cardiac Surgery, Frankel Cardiovascular Center, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Paul Tang
- Department of Cardiac Surgery, Frankel Cardiovascular Center, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Y Eugene Chen
- Department of Cardiac Surgery, Frankel Cardiovascular Center, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhong Wang
- Department of Cardiac Surgery, Frankel Cardiovascular Center, The University of Michigan, Ann Arbor, MI 48109, USA.
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Miao M, Shi X, Zheng X, Wu B, Miao Y. Characterization of SIPs-type aquaporins and their roles in response to environmental cues in rice (Oryza sativa L.). BMC PLANT BIOLOGY 2024; 24:305. [PMID: 38644479 PMCID: PMC11034084 DOI: 10.1186/s12870-024-05002-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 04/09/2024] [Indexed: 04/23/2024]
Abstract
BACKGROUND Aquaporins (AQPs) facilitate water diffusion across biological membranes and are involved in all phases of growth and development. Small and basic intrinsic proteins (SIPs) belong to the fourth subfamily of the plant AQPs. Although SIPs are widely present in higher plants, reports on SIPs are limited. Rice is one of the major food crops in the world, and water use is an important factor affecting rice growth and development; therefore, this study aimed to provide information relevant to the function and environmental response of the rice SIP gene family. RESULTS The rice (Oryza sativa L. japonica) genome encodes two SIP-like genes, OsSIP1 and OsSIP2, whose products are predominantly located in the endoplasmic reticulum (ER) membrane but transient localization to the plasma membrane is not excluded. Heterologous expression in a yeast aquaglyceroporin-mutant fps1Δ showed that both OsSIP1 and OsSIP2 made the cell more sensitive to KCl, sorbitol and H2O2, indicating facilitated permeation of water and hydrogen peroxide. In addition, the yeast cells expressing OsSIP2 were unable to efflux the toxic methylamine taken up by the endogenous MEP permeases, but OsSIP1 showed subtle permeability to methylamine, suggesting that OsSIP1 may have a wider conducting pore than OsSIP2. Expression profiling in different rice tissues or organs revealed that OsSIP1 was expressed in all tissues tested, whereas OsSIP2 was preferentially expressed in anthers and weakly expressed in other tissues. Consistent with this, histochemical staining of tissues expressing the promoter-β-glucuronidase fusion genes revealed their tissue-specific expression profile. In rice seedlings, both OsSIPs were upregulated to varied levels under different stress conditions, including osmotic shock, high salinity, unfavorable temperature, redox challenge and pathogen attack, as well as by hormonal treatments such as GA, ABA, MeJA, SA. However, a reduced expression of both OsSIPs was observed under dehydration treatment. CONCLUSIONS Our results suggest that SIP-like aquaporins are not restricted to the ER membrane and are likely to be involved in unique membrane functions in substrate transport, growth and development, and environmental response.
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Affiliation(s)
- Miao Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Ximiao Shi
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Xiangzi Zheng
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Binghua Wu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China.
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Rabi LT, Valente DZ, de Souza Teixeira E, Peres KC, de Oliveira Almeida M, Bufalo NE, Ward LS. Potential new cancer biomarkers revealed by quantum chemistry associated with bioinformatics in the study of selectin polymorphisms. Heliyon 2024; 10:e28830. [PMID: 38586333 PMCID: PMC10998122 DOI: 10.1016/j.heliyon.2024.e28830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024] Open
Abstract
Understanding the complex mechanisms involved in diseases caused by or related to important genetic variants has led to the development of clinically useful biomarkers. However, the increasing number of described variants makes it difficult to identify variants worthy of investigation, and poses challenges to their validation. We combined publicly available datasets and open source robust bioinformatics tools with molecular quantum chemistry methods to investigate the involvement of selectins, important molecules in the cell adhesion process that play a fundamental role in the cancer metastasis process. We applied this strategy to investigate single nucleotide variants (SNPs) in the intronic and UTR regions and missense SNPs with amino acid changes in the SELL, SELP, SELE, and SELPLG genes. We then focused on thyroid cancer, seeking these SNPs potential to identify biomarkers for susceptibility, diagnosis, prognosis, and therapeutic targets. We demonstrated that SELL gene polymorphisms rs2229569, rs1131498, rs4987360, rs4987301 and rs2205849; SELE gene polymorphisms rs1534904 and rs5368; rs3917777, rs2205894 and rs2205893 of SELP gene; and rs7138370, rs7300972 and rs2228315 variants of SELPLG gene may produce important alterations in the DNA structure and consequent changes in the morphology and function of the corresponding proteins. In conclusion, we developed a strategy that may save valuable time and resources in future investigations, as we were able to provide a solid foundation for the selection of selectin gene variants that may become important biomarkers and deserve further investigation in cancer patients. Large-scale clinical studies in different ethnic populations and laboratory experiments are needed to validate our results.
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Affiliation(s)
- Larissa Teodoro Rabi
- Laboratory of Cancer Molecular Genetics, Faculty of Medical Sciences, State University of Campinas (UNI-CAMP), Campinas, SP, Brazil
- .Department of Biomedicine, Nossa Senhora do Patrocínio University Center (CEUNSP), Itu, SP, Brazil
- Institute of Health Sciences, Paulista University (UNIP), Campinas, SP, Brazil
| | - Davi Zanoni Valente
- Laboratory of Cancer Molecular Genetics, Faculty of Medical Sciences, State University of Campinas (UNI-CAMP), Campinas, SP, Brazil
| | - Elisangela de Souza Teixeira
- Laboratory of Cancer Molecular Genetics, Faculty of Medical Sciences, State University of Campinas (UNI-CAMP), Campinas, SP, Brazil
| | - Karina Colombera Peres
- Laboratory of Cancer Molecular Genetics, Faculty of Medical Sciences, State University of Campinas (UNI-CAMP), Campinas, SP, Brazil
- Department of Medicine, Max Planck University Center, Campinas, SP, Brazil
| | | | - Natassia Elena Bufalo
- Laboratory of Cancer Molecular Genetics, Faculty of Medical Sciences, State University of Campinas (UNI-CAMP), Campinas, SP, Brazil
- Department of Medicine, Max Planck University Center, Campinas, SP, Brazil
- Department of Medicine, São Leopoldo Mandic and Research Center, Campinas, SP, Brazil
| | - Laura Sterian Ward
- Laboratory of Cancer Molecular Genetics, Faculty of Medical Sciences, State University of Campinas (UNI-CAMP), Campinas, SP, Brazil
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Liu Y, Si W, Fu S, Wang J, Cheng T, Zhang Q, Pan H. PfPIN5 promotes style elongation by regulating cell length in Primula forbesii Franch. ANNALS OF BOTANY 2024; 133:473-482. [PMID: 38190350 PMCID: PMC11006536 DOI: 10.1093/aob/mcae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/06/2024] [Indexed: 01/10/2024]
Abstract
BACKGROUND AND AIMS Style dimorphism is one of the polymorphic characteristics of flowers in heterostylous plants, which have two types of flowers: the pin morph, with long styles and shorter anthers, and the thrum morph, with short styles and longer anthers. The formation of dimorphic styles has received attention in the plant world. Previous studies showed that CYP734A50 in Primula determined style length and limited style elongation and that the brassinosteroid metabolic pathway was involved in regulation of style length. However, it is unknown whether there are other factors affecting the style length of Primula. METHODS Differentially expressed genes highly expressed in pin morph styles were screened based on Primula forbesii transcriptome data. Virus-induced gene silencing was used to silence these genes, and the style length and anatomical changes were observed 20 days after injection. KEY RESULTS PfPIN5 was highly expressed in pin morph styles. When PfPIN5 was silenced, the style length was shortened in pin and long-homostyle plants by shortening the length of style cells. Moreover, silencing CYP734A50 in thrum morph plants increased the expression level of PfPIN5 significantly, and the style length increased. The results indicated that PfPIN5, an auxin efflux transporter gene, contributed to regulation of style elongation in P. forbesii. CONCLUSIONS The results implied that the auxin pathway might also be involved in the formation of styles of P. forbesii, providing a new pathway for elucidating the molecular mechanism of style elongation in P. forbesii.
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Affiliation(s)
- Ying Liu
- State Key Laboratory of Efficient Production of Forest Resources; Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture; College of Landscape Architecture, Beijing Forestry University, Beijing 100083, P. R. China
| | - Weijia Si
- State Key Laboratory of Efficient Production of Forest Resources; Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture; College of Landscape Architecture, Beijing Forestry University, Beijing 100083, P. R. China
| | - Sitong Fu
- State Key Laboratory of Efficient Production of Forest Resources; Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture; College of Landscape Architecture, Beijing Forestry University, Beijing 100083, P. R. China
| | - Jia Wang
- State Key Laboratory of Efficient Production of Forest Resources; Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture; College of Landscape Architecture, Beijing Forestry University, Beijing 100083, P. R. China
| | - Tangren Cheng
- State Key Laboratory of Efficient Production of Forest Resources; Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture; College of Landscape Architecture, Beijing Forestry University, Beijing 100083, P. R. China
| | - Qixiang Zhang
- State Key Laboratory of Efficient Production of Forest Resources; Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture; College of Landscape Architecture, Beijing Forestry University, Beijing 100083, P. R. China
| | - Huitang Pan
- State Key Laboratory of Efficient Production of Forest Resources; Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture; College of Landscape Architecture, Beijing Forestry University, Beijing 100083, P. R. China
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Singh RK, Chaurasiya AK, Kumar A. Ab initio modeling of human IRS1 protein to find novel target to dock with drug MH to mitigate T2DM diabetes by insulin signaling. 3 Biotech 2024; 14:108. [PMID: 38476643 PMCID: PMC10925585 DOI: 10.1007/s13205-024-03955-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 02/03/2024] [Indexed: 03/14/2024] Open
Abstract
IRS1 is a cytoplasmic adaptor protein that helps in cellular growth, glucose metabolism, proliferation, and differentiation. Highly disordered (insulin receptor substrate 1) IRS1 protein sequence (mol.wt- 131,590.97 da) has been used to develop model using ab initio modeling technique by I-Tassar tool and Discovery Studio/ DogSite Server to decipher a novel active site. The constructed protein model has been submitted with PMDB Id- PM0082210. GRAVY index of IRS1 model ( - 0.675) indicated surface protein-water interaction. Protparam tool instability index (75.22) demonstrated disorderedness combined with loops owing to prolines/glycines. After refinement, the Ramachandran plot showed that 88 percent of AAs were present in the allowed region and only 0.5% in the disallowed region. Novel IRS1 model protein has 10 α-helices, 22 β-sheets, 20 β-hairpins, 5 β-bulges, 47 strands, 105 β-turns, and 8 γ-turns. Docking of IRS1 with drug MH demonstrated interaction of Ser-70, Thr-18, and Pro-69 with C-H bonds; Gln-71, and Glu-113 with hydrogen bonds; while both Glu-114 and Glu-113 with salt-bridge connection. Permissible 1.0-1.5 Å range of RMSD fluctuation between 20 and 45 ns was obtained in simulation of IRS1 and IRS1-met complex confirmed that both complexes were stable during whole simulation process. RMSF result showed that except positions 57AA and 114AA, the binding of drug had no severe effects on the flexibility of the IRS1 and IRS1-met complex. The RoG value of compactness and rigidity showed little change in IRS1 protein. SASA value of IRS1 indicated non-significant fluctuation between IRS1 and drug MH means ligand (drug) and IRS1 receptor form stable structure. Hydrogen bond strength of IRS1 and IRS1-met was 81.2 and 76.4, respectively, which suggested stable interaction.
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Affiliation(s)
- Ritika Kumari Singh
- School of Biotechnology, Institute of Science, BHU, Varanasi, Uttar Pradesh 221005 India
| | | | - Arvind Kumar
- School of Biotechnology, Institute of Science, BHU, Varanasi, Uttar Pradesh 221005 India
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Hendi NN, Nemer G. In silico characterization of the novel SDR42E1 as a potential vitamin D modulator. J Steroid Biochem Mol Biol 2024; 238:106447. [PMID: 38160768 DOI: 10.1016/j.jsbmb.2023.106447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
The short-chain dehydrogenase/reductase (SDR) superfamily encompasses enzymes that play essential roles in the metabolism of steroid hormones and lipids. Despite an enigmatic function, recent genetic studies have linked the novel SDR 42 extended-1 (SDR42E1) gene to 25-hydroxyvitamin D levels. This study investigated the potential SDR42E1 functions and interactions with vitamin D using bioinformatics and molecular docking studies. Phylogenetic analysis unveiled that the nucleotide sequences of human SDR42E1 exhibit high evolutionary conservation across nematodes and fruit flies. Molecular docking analysis identified strong binding affinities between SDR42E1 and its orthologs with vitamin D3 and essential precursors, 8-dehydrocholesterol, followed by 7-dehydrocholesterol and 25-hydroxyvitamin D. The hydrophobic interactions observed between the protein residues and vitamin D compounds supported the predicted transmembrane localization of SDR42E1. Our investigation provides valuable insights into the potential role of SDR42E1 in skin vitamin D biosynthesis throughout species. This provides the foundation for future research and development of targeted therapies for vitamin D deficiency and related health conditions.
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Affiliation(s)
- Nagham Nafiz Hendi
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar
| | - Georges Nemer
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar; Department of Biochemistry and Molecular Genetics, American University of Beirut, P.O. Box 110236, Beirut, Lebanon.
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Maghraby A, Alzalaty M. Genome-wide identification and evolutionary analysis of the AP2/EREBP, COX and LTP genes in Zea mays L. under drought stress. Sci Rep 2024; 14:7610. [PMID: 38556556 PMCID: PMC10982304 DOI: 10.1038/s41598-024-57376-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 03/18/2024] [Indexed: 04/02/2024] Open
Abstract
AP2 (APETALA2)/EREBP (ethylene-responsive element-binding protein), cytochrome c oxidase (COX) and nonspecific lipid transfer proteins (LTP) play important roles in the response to drought stress. This is the first study to identify the COX gene in Zea mays L. via genome-wide analysis. The qRT‒PCR results indicated that AP2/EREBP, COX and LTP were downregulated, with fold changes of 0.84, 0.53 and 0.31, respectively, after 12 h of drought stress. Genome-wide analysis identified 78 AP2/EREBP, 6 COX and 10 LTP genes in Z. mays L. Domain analysis confirmed the presence of the AP2 domain, Cyt_c_Oxidase_Vb domain and nsLTP1 in the AP2/EREBP, COX and LTP proteins, respectively. The AP2/EREBP protein family (AP2) includes five different domain types: the AP2/ERF domain, the EREBP-like factor (EREBP), the ethylene responsive factor (ERF), the dehydration responsive element binding protein (DREB) and the SHN SHINE. Synteny analysis of the AP2/EREBP, COX and LTP genes revealed collinearity orthologous relationships in O. sativa, H. vulgare and A. thaliana. AP2/EREBP genes were found on the 10 chromosomes of Z. mays L. COX genes were found on chromosomes 1, 3, 4, 5, 7 and 8. LTP genes were found on chromosomes 1, 3, 6, 8, 9 and 10. In the present study, the Ka/Ks ratios of the AP2/EREBP paralogous pairs indicated that the AP2/EREBP genes were influenced primarily by purifying selection, which indicated that the AP2/EREBP genes received strong environmental pressure during evolution. The Ka/Ks ratios of the COX-3/COX-4 paralogous pairs indicate that the COX-3/COX-4 genes were influenced primarily by Darwinian selection (driving change). For the LTP genes, the Ka/Ks ratios of the LTP-1/LTP-10, LTP-5/LTP-3 and LTP-4/LTP-8 paralogous pairs indicate that these genes were influenced primarily by purifying selection, while the Ka/Ks ratios of the LTP-2/LTP-6 paralogous pairs indicate that these genes were influenced primarily by Darwinian selection. The duplication time of the AP2/EREBP paralogous gene pairs in Z. mays L. ranged from approximately 9.364 to 100.935 Mya. The duplication time of the COX-3/COX-4 paralogous gene pair was approximately 5.217 Mya. The duplication time of the LTP paralogous gene pairs ranged from approximately 19.064 to 96.477 Mya. The major focus of research is to identify the genes that are responsible for drought stress tolerance to improve maize for drought stress tolerance. The results of the present study will improve the understanding of the functions of the AP2/EREBP, COX and LTP genes in response to drought stress.
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Affiliation(s)
- Amaal Maghraby
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt.
| | - Mohamed Alzalaty
- Department of Plant Genetic Transformation, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
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Sun S, Zhao B, Li J, Zhang X, Yao S, Bao Z, Cai J, Yang J, Chen Y, Wu X. Regulation of Hair Follicle Growth and Development by Different Alternative Spliceosomes of FGF5 in Rabbits. Genes (Basel) 2024; 15:409. [PMID: 38674344 PMCID: PMC11049220 DOI: 10.3390/genes15040409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/23/2024] [Accepted: 03/24/2024] [Indexed: 04/28/2024] Open
Abstract
This study investigated the regulatory effect of alternative spliceosomes of the fibroblast growth factor 5 (FGF5) gene on hair follicle (HF) growth and development in rabbits. The FGF5 alternative spliceosomes (called FGF5-X1, FGF5-X2, FGF5-X3) were cloned. The overexpression vector and siRNA of spliceosomes were transfected into dermal papilla cells (DPCs) to analyze the regulatory effect on DPCs. The results revealed that FGF5-X2 and FGF5-X3 overexpression significantly decreased LEF1 mRNA expression (p < 0.01). FGF5-X1 overexpression significantly reduced CCND1 expression (p < 0.01). FGF5-X1 and FGF5-X2 possibly downregulated the expression level of FGF2 mRNA (p < 0.05), and FGF5-X3 significantly downregulated the expression level of FGF2 mRNA (p < 0.01). The FGF5 alternative spliceosomes significantly downregulated the BCL2 mRNA expression level in both cases (p < 0.01). FGF5-X1 and FGF5-X2 significantly increased TGFβ mRNA expression (p < 0.01). All three FGF5 alternative spliceosomes inhibited DPC proliferation. In conclusion, the expression profile of HF growth and development-related genes can be regulated by FGF5 alternative spliceosomes, inhibiting the proliferation of DPCs and has an influence on the regulation of HF growth in rabbits. This study provides insights to further investigate the mechanism of HF development in rabbits via FGF5 regulation.
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Affiliation(s)
- Shaoning Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Bohao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Jiali Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Xiyu Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Shuyu Yao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Zhiyuan Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Jiawei Cai
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Jie Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Yang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
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Zahiri Z, Mehrshad N, Mehrshad M. DF-Phos: Prediction of Protein Phosphorylation Sites by Deep Forest. J Biochem 2024; 175:447-456. [PMID: 38153271 DOI: 10.1093/jb/mvad116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/29/2023] Open
Abstract
Phosphorylation is the most important and studied post-translational modification (PTM), which plays a crucial role in protein function studies and experimental design. Many significant studies have been performed to predict phosphorylation sites using various machine-learning methods. Recently, several studies have claimed that deep learning-based methods are the best way to predict the phosphorylation sites because deep learning as an advanced machine learning method can automatically detect complex representations of phosphorylation patterns from raw sequences and thus offers a powerful tool to improve phosphorylation site prediction. In this study, we report DF-Phos, a new phosphosite predictor based on the Deep Forest to predict phosphorylation sites. In DF-Phos, the feature vector taken from the CkSAApair method is as input for a Deep Forest framework for predicting phosphorylation sites. The results of 10-fold cross-validation show that the Deep Forest method has the highest performance among other available methods. We implemented a Python program of DF-Phos, which is freely available for non-commercial use at https://github.com/zahiriz/DF-Phos Moreover, users can use it for various PTM predictions.
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Affiliation(s)
- Zeynab Zahiri
- Faculty of Electrical and Computer Engineering, University of Birjand, Birjand, Iran
| | - Nasser Mehrshad
- Faculty of Electrical and Computer Engineering, University of Birjand, Birjand, Iran
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, 750 07 Sweden
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Diep DTV, Collado J, Hugenroth M, Fausten RM, Percifull L, Wälte M, Schuberth C, Schmidt O, Fernández-Busnadiego R, Bohnert M. A metabolically controlled contact site between vacuoles and lipid droplets in yeast. Dev Cell 2024; 59:740-758.e10. [PMID: 38367622 DOI: 10.1016/j.devcel.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 11/17/2023] [Accepted: 01/18/2024] [Indexed: 02/19/2024]
Abstract
The lipid droplet (LD) organization proteins Ldo16 and Ldo45 affect multiple aspects of LD biology in yeast. They are linked to the LD biogenesis machinery seipin, and their loss causes defects in LD positioning, protein targeting, and breakdown. However, their molecular roles remained enigmatic. Here, we report that Ldo16/45 form a tether complex with Vac8 to create vacuole lipid droplet (vCLIP) contact sites, which can form in the absence of seipin. The phosphatidylinositol transfer protein (PITP) Pdr16 is a further vCLIP-resident recruited specifically by Ldo45. While only an LD subpopulation is engaged in vCLIPs at glucose-replete conditions, nutrient deprivation results in vCLIP expansion, and vCLIP defects impair lipophagy upon prolonged starvation. In summary, Ldo16/45 are multifunctional proteins that control the formation of a metabolically regulated contact site. Our studies suggest a link between LD biogenesis and breakdown and contribute to a deeper understanding of how lipid homeostasis is maintained during metabolic challenges.
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Affiliation(s)
- Duy Trong Vien Diep
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Javier Collado
- Institute of Neuropathology, University Medical Center Göttingen, 37099 Göttingen, Germany
| | - Marie Hugenroth
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Rebecca Martina Fausten
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Louis Percifull
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Mike Wälte
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany
| | - Christian Schuberth
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Oliver Schmidt
- Institute of Cell Biology, Biocenter Innsbruck, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Rubén Fernández-Busnadiego
- Institute of Neuropathology, University Medical Center Göttingen, 37099 Göttingen, Germany; Cluster of Excellence "Multiscale Imaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Faculty of Physics, University of Göttingen, Göttingen 37077, Germany
| | - Maria Bohnert
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany.
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de Carvalho RSA, Rasel SI, Khandelwal NK, Tomasiak TM. Cryo-EM structure of the tetra-phosphorylated R-domain in Ycf1 reveals key interactions for transport regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583773. [PMID: 38496555 PMCID: PMC10942426 DOI: 10.1101/2024.03.06.583773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Many ATP-binding cassette (ABC) transporters are regulated by phosphorylation on long and disordered loops which present a challenge to visualize with structural methods. We have trapped an activated state of the regulatory domain (R-domain) of Yeast Cadmium Factor 1 (Ycf1) by enzymatically enriching the phosphorylated state. A 3.2 Å cryo-EM structure reveals an R-domain structure with four phosphorylated residues and a position for the entire R-domain. The structure reveals key R-domain interactions including a bridging interaction between NBD1 and NBD2 as well as an interaction with the R-insertion, another regulatory region. We systematically probe these interactions with a linker substitution strategy along the R-domain and find a close match with these interactions and survival under Ycf1-dependent growth conditions. We propose a model where four overlapping phosphorylation sites bridge several regions of Ycf1 to engage in a transport-competent state.
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Affiliation(s)
| | - Shamiul I Rasel
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | - Nitesh K Khandelwal
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
- Current Address: Department of Biochemistry and Biophysics, University of California - San Francisco, San Francisco, CA 94
| | - Thomas M Tomasiak
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
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48
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Fasawe AS, Adams JM, Engelke MF. KIF3A tail domain phosphorylation is not required for ciliogenesis in mouse embryonic fibroblasts. iScience 2024; 27:109149. [PMID: 38405607 PMCID: PMC10884758 DOI: 10.1016/j.isci.2024.109149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/21/2023] [Accepted: 02/01/2024] [Indexed: 02/27/2024] Open
Abstract
Primary cilia are essential signaling organelles that protrude from most cells in the body. Heterodimeric kinesin-2 (KIF3A/KIF3B/KAP3) powers several intracellular transport processes, including intraflagellar transport (IFT), essential for ciliogenesis. A long-standing question is how a motor protein is differentially regulated for specific cargos. Since phosphorylation of the KIF3A tail domain was suggested to regulate the activity of kinesin-2 for ciliogenesis, similarly as for the cytosolic cargo N-Cadherin, we set out to map the phosphosites involved in this regulation. Using well-characterized Kif3a-/-; Kif3b-/- mouse embryonic fibroblasts, we performed ciliogenesis rescue assays with a library of phosphomimetic mutants comprising all predicted phosphosites in the KIF3A tail domain. In contrast to previous reports, we found that KIF3A tail domain phosphorylation is dispensable for ciliogenesis in mammals. Thus, mammalian kinesin-2 is differently regulated for IFT than currently thought, consistent with the idea of differential regulation for ciliary and cytosolic cargo.
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Affiliation(s)
- Ayoola S. Fasawe
- School of Biological Sciences, Cell Physiology, Illinois State University, Normal, IL 61790, USA
| | - Jessica M. Adams
- School of Biological Sciences, Cell Physiology, Illinois State University, Normal, IL 61790, USA
| | - Martin F. Engelke
- School of Biological Sciences, Cell Physiology, Illinois State University, Normal, IL 61790, USA
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Shaji F, Mohanan NK, Shahzad S, V P G, Bangalore Prabhashankar A, Sundaresan NR, Laishram RS. Proto-oncogene cSrc-mediated RBM10 phosphorylation arbitrates anti-hypertrophy gene program in the heart and controls cardiac hypertrophy. Life Sci 2024; 341:122482. [PMID: 38309577 DOI: 10.1016/j.lfs.2024.122482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/20/2024] [Accepted: 01/29/2024] [Indexed: 02/05/2024]
Abstract
AIMS RBM10 is a well-known RNA binding protein that regulates alternative splicing in various disease states. We have shown a splicing-independent function of RBM10 that regulates heart failure. This study aims to unravel a new biological function of RBM10 phosphorylation by proto-oncogene cSrc that enables anti-hypertrophy gene program and controls cardiac hypertrophy. MATERIALS AND METHODS We employ in vitro and in vivo approaches to characterise RBM10 phosphorylation at three-tyrosine residues (Y81, Y500, and Y971) by cSrc and target mRNA regulation. We also use isoproterenol induced rat heart and cellular hypertrophy model to determine role of cSrc-mediated RBM10 phosphorylation. KEY FINDINGS We show that RBM10 phosphorylation is induced in cellular and animal heart model of cardiac hypertrophy and regulates target mRNA expression and 3'-end formation. Inhibition of cSrc kinase or mutation of the three-tyrosine phosphorylation sites to phenylalanine accentuates myocyte hypertrophy, and results in advancement and an early attainment of hypertrophy in the heart. RBM10 is down regulated in the hypertrophic myocyte and that its re-expression reverses cellular and molecular changes in the myocyte. However, in the absence of phosphorylation (cSrc inhibition or phospho-deficient mutation), restoration of endogenous RBM10 level in the hypertrophic heart or ectopic re-expression in vitro failed to reverse cardiomyocyte hypertrophy. Mechanistically, loss of RBM10 phosphorylation inhibits nuclear localisation and interaction with Star-PAP compromising anti-hypertrophy gene expression. SIGNIFICANCE Our study establishes that cSrc-mediated RBM10 phosphorylation arbitrates anti-hypertrophy gene program. We also report a new functional regulation of RBM10 by phosphorylation that is poised to control heart failure.
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Affiliation(s)
- Feba Shaji
- Rajiv Gandhi Centre for Biotechnology, Cardiovascular Diseases and Diabetes Biology Group, Thiruvananthapuram, 695014, India; Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Neeraja K Mohanan
- Rajiv Gandhi Centre for Biotechnology, Cardiovascular Diseases and Diabetes Biology Group, Thiruvananthapuram, 695014, India; Manipal Academy of Higher Education, 576104, India
| | - Sumayya Shahzad
- Rajiv Gandhi Centre for Biotechnology, Cardiovascular Diseases and Diabetes Biology Group, Thiruvananthapuram, 695014, India
| | - Gowri V P
- Rajiv Gandhi Centre for Biotechnology, Cardiovascular Diseases and Diabetes Biology Group, Thiruvananthapuram, 695014, India
| | | | | | - Rakesh S Laishram
- Rajiv Gandhi Centre for Biotechnology, Cardiovascular Diseases and Diabetes Biology Group, Thiruvananthapuram, 695014, India.
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50
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Niphadkar S, Karinje L, Laxman S. The PP2A-like phosphatase Ppg1 mediates assembly of the Far complex to balance gluconeogenic outputs and enables adaptation to glucose depletion. PLoS Genet 2024; 20:e1011202. [PMID: 38452140 PMCID: PMC10950219 DOI: 10.1371/journal.pgen.1011202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/19/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
To sustain growth in changing nutrient conditions, cells reorganize outputs of metabolic networks and appropriately reallocate resources. Signaling by reversible protein phosphorylation can control such metabolic adaptations. In contrast to kinases, the functions of phosphatases that enable metabolic adaptation as glucose depletes are poorly studied. Using a Saccharomyces cerevisiae deletion screen, we identified the PP2A-like phosphatase Ppg1 as required for appropriate carbon allocations towards gluconeogenic outputs-trehalose, glycogen, UDP-glucose, UDP-GlcNAc-after glucose depletion. This Ppg1 function is mediated via regulation of the assembly of the Far complex-a multi-subunit complex that tethers to the ER and mitochondrial outer membranes forming localized signaling hubs. The Far complex assembly is Ppg1 catalytic activity-dependent. Ppg1 regulates the phosphorylation status of multiple ser/thr residues on Far11 to enable the proper assembly of the Far complex. The assembled Far complex is required to maintain gluconeogenic outputs after glucose depletion. Glucose in turn regulates Far complex amounts. This Ppg1-mediated Far complex assembly, and Ppg1-Far complex dependent control of gluconeogenic outputs enables adaptive growth under glucose depletion. Our study illustrates how protein dephosphorylation is required for the assembly of a multi-protein scaffold present in localized cytosolic pools, to thereby alter gluconeogenic flux and enable cells to metabolically adapt to nutrient fluctuations.
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Affiliation(s)
- Shreyas Niphadkar
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Lavanya Karinje
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
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