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Li B, Ustyugova IV, Szymkowicz L, Zhu S, Ming M, Fung KYY, Cortés G, James DA, Hrynyk M, Rahman N, Brookes RH, Ausar SF. Formulation development of a stable influenza recombinant neuraminidase vaccine candidate. Hum Vaccin Immunother 2024; 20:2304393. [PMID: 38497413 PMCID: PMC10950269 DOI: 10.1080/21645515.2024.2304393] [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: 10/25/2023] [Accepted: 01/09/2024] [Indexed: 03/19/2024] Open
Abstract
Current influenza vaccines could be augmented by including recombinant neuraminidase (rNA) protein antigen to broaden protective immunity and improve efficacy. Toward this goal, we investigated formulation conditions to optimize rNA physicochemical stability. When rNA in sodium phosphate saline buffer (NaPBS) was frozen and thawed (F/T), the tetrameric structure transitioned from a "closed" to an "open" conformation, negatively impacting functional activity. Hydrogen deuterium exchange experiments identified differences in anchorage binding sites at the base of the open tetramer, offering a structural mechanistic explanation for the change in conformation and decreased functional activity. Change to the open configuration was triggered by the combined stresses of acidic pH and F/T. The desired closed conformation was preserved in a potassium phosphate buffer (KP), minimizing pH drop upon freezing and including 10% sucrose to control F/T stress. Stability was further evaluated in thermal stress studies where changes in conformation were readily detected by ELISA and size exclusion chromatography (SEC). Both tests were suitable indicators of stability and antigenicity and considered potential critical quality attributes (pCQAs). To understand longer-term stability, the pCQA profiles from thermally stressed rNA at 6 months were modeled to predict stability of at least 24-months at 5°C storage. In summary, a desired rNA closed tetramer was maintained by formulation selection and monitoring of pCQAs to produce a stable rNA vaccine candidate. The study highlights the importance of understanding and controlling vaccine protein structural and functional integrity.
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Affiliation(s)
- Bing Li
- Sanofi Global Vaccine Drug Product Development, Toronto, ON, Canada
| | | | | | | | - Marin Ming
- Sanofi Analytical Sciences, Toronto, ON, Canada
| | - Karen Y. Y. Fung
- Sanofi Global Vaccine Drug Product Development, Toronto, ON, Canada
| | - Guadalupe Cortés
- Sanofi mRNA & Translational Medicine COVID Franchise, Global Clinical Development, Waltham, MA, USA
| | - D. Andrew James
- Sanofi External Research and Development, Toronto, ON, Canada
| | | | - Nausheen Rahman
- Sanofi Global Vaccine Drug Product Development, Toronto, ON, Canada
| | - Roger H. Brookes
- Sanofi Global Vaccine Drug Product Development, Toronto, ON, Canada
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Li D, Li H, Feng H, Qi P, Wu Z. Unveiling kiwifruit TCP genes: evolution, functions, and expression insights. PLANT SIGNALING & BEHAVIOR 2024; 19:2338985. [PMID: 38597293 PMCID: PMC11008546 DOI: 10.1080/15592324.2024.2338985] [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: 02/21/2024] [Accepted: 03/26/2024] [Indexed: 04/11/2024]
Abstract
The TEOSINTE-BRANCHED1/CYCLOIDEA/PROLEFERATING-CELL-FACTORS (TCP) gene family is a plant-specific transcriptional factor family involved in leaf morphogenesis and senescence, lateral branching, hormone crosstalk, and stress responses. To date, a systematic study on the identification and characterization of the TCP gene family in kiwifruit has not been reported. Additionally, the function of kiwifruit TCPs in regulating kiwifruit responses to the ethylene treatment and bacterial canker disease pathogen (Pseudomonas syringae pv. actinidiae, Psa) has not been investigated. Here, we identified 40 and 26 TCP genes in Actinidia chinensis (Ac) and A. eriantha (Ae) genomes, respectively. The synteny analysis of AcTCPs illustrated that whole-genome duplication accounted for the expansion of the TCP family in Ac. Phylogenetic, conserved domain, and selection pressure analysis indicated that TCP family genes in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in TCP gene number and distribution. Our results also suggested that protein structure and cis-element architecture in promoter regions of TCP genes have driven the function divergence of duplicated gene pairs. Three and four AcTCP genes significantly affected kiwifruit responses to the ethylene treatment and Psa invasion, respectively. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit TCPs.
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Affiliation(s)
- Donglin Li
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Haibo Li
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Huimin Feng
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Ping Qi
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Zhicheng Wu
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
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Kajsikova M, Kajsik M, Bocanova L, Papayova K, Drahovska H, Bukovska G. Endolysin EN572-5 as an alternative to treat urinary tract infection caused by Streptococcus agalactiae. Appl Microbiol Biotechnol 2024; 108:79. [PMID: 38189950 PMCID: PMC10774192 DOI: 10.1007/s00253-023-12949-8] [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: 08/14/2023] [Revised: 11/13/2023] [Accepted: 11/26/2023] [Indexed: 01/09/2024]
Abstract
Streptococcus agalactiae (Group B Streptococcus, GBS) is an opportunistic pathogen causing urinary tract infection (UTI). Endolysin EN572-5 was identified in prophage KMB-572-E of the human isolate Streptococcus agalactiae KMB-572. The entire EN572-5 gene was cloned into an expression vector and the corresponding recombinant protein EN572-5 was expressed in Escherichia coli in a soluble form, isolated by affinity chromatography, and characterized. The isolated protein was highly active after 30 min incubation in a temperature range of - 20 °C to 37 °C and in a pH range of 5.5-8.0. The endolysin EN572-5 lytic activity was tested on different Streptococcus spp. and Lactobacillus spp. The enzyme lysed clinical GBS (n = 31/31) and different streptococci (n = 6/8), and also exhibited moderate lytic activity against UPEC (n = 4/4), but no lysis of beneficial vaginal lactobacilli (n = 4) was observed. The ability of EN572-5 to eliminate GBS during UTI was investigated using an in vitro model of UPSA. After the administration of 3 μM EN572-5, a nearly 3-log decrease of urine bacterial burden was detected within 3 h. To date, no studies have been published on the use of endolysins against S. agalactiae during UTI. KEY POINTS: • A lytic protein, EN572-5, from a prophage of a human GBS isolate has been identified. • This protein is easily produced, simple to prepare, and stable after lyophilization. • The bacteriolytic activity of EN572-5 was demonstrated for the first time in human urine.
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Affiliation(s)
- Maria Kajsikova
- Department of Genomics and Biotechnology, Institute of Molecular Biology SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Michal Kajsik
- Comenius University Science Park, Ilkovicova 8, 841 04, Bratislava, Slovakia
| | - Lucia Bocanova
- Department of Genomics and Biotechnology, Institute of Molecular Biology SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Kristina Papayova
- Department of Genomics and Biotechnology, Institute of Molecular Biology SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Hana Drahovska
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 841 15, Bratislava, Slovakia
| | - Gabriela Bukovska
- Department of Genomics and Biotechnology, Institute of Molecular Biology SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia.
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Li R, Zhu X, Zhang P, Wu X, Jin Q, Pan J. Ser/Thr protein kinase Stk1 phosphorylates the key transcriptional regulator AlgR to modulate virulence and resistance in Pseudomonas aeruginosa. Virulence 2024; 15:2367649. [PMID: 38898809 PMCID: PMC11197903 DOI: 10.1080/21505594.2024.2367649] [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: 01/25/2024] [Accepted: 06/09/2024] [Indexed: 06/21/2024] Open
Abstract
Pseudomonas aeruginosa is one of the leading causes of nosocomial infections worldwide and has emerged as a serious public health threat, due in large part to its multiple virulence factors and remarkable resistance capabilities. Stk1, a eukaryotic-type Ser/Thr protein kinase, has been shown in our previous work to be involved in the regulation of several signalling pathways and biological processes. Here, we demonstrate that deletion of stk1 leads to alterations in several virulence- and resistance-related physiological functions, including reduced pyocyanin and pyoverdine production, attenuated twitching motility, and enhanced biofilm production, extracellular polysaccharide secretion, and antibiotic resistance. Moreover, we identified AlgR, an important transcriptional regulator, as a substrate for Stk1, with its phosphorylation at the Ser143 site catalysed by Stk1. Intriguingly, both the deletion of stk1 and the mutation of Ser143 of AlgR to Ala result in similar changes in the above-mentioned physiological functions. Furthermore, assays of algR expression in these strains suggest that changes in the phosphorylation state of AlgR, rather than its expression level, underlie changes in these physiological functions. These findings uncover Stk1-mediated phosphorylation of AlgR as an important mechanism for regulating virulence and resistance in P. aeruginosa.
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Affiliation(s)
- Rui Li
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Xuan Zhu
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Pengfei Zhang
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Xuan Wu
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Qian Jin
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jianyi Pan
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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Ramesh Sawant A, Pagal S, Prashanth K. Role of the NtrC family response regulator in nitrogen metabolism of Acinetobacter baumannii. Gene 2024; 924:148552. [PMID: 38734189 DOI: 10.1016/j.gene.2024.148552] [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: 12/29/2023] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
Acinetobacter baumannii is an important Gram-negative nosocomial pathogen that causes opportunistic infections and employs different mechanisms to survive in the presence of antibiotics in the host. Nutrient limitation is one of the important defense mechanisms of the mammalian immune system to fight against the colonization of pathogens like A. baumannii. The present study describes an NtrC-type Response Regulator (RR) A1S_1978 involved in modulating the metabolism and cell morphology of A. baumannii via a two-component system. This RR was found to be highly conserved in the Acinetobacter and other important Gram-negative pathogens. Sequence analysis reveals that this RR contains an HTH_8 DNA-binding domain. It is also observed that deletion of this RR resulted in elongated cell phenotype and altered colony morphology of A. baumannii. We showed that the ability of A. baumannii to form biofilm and pellicle is partly abolished upon deletion of this response regulator. We showed that mutant strains lacking RR A1S_1978 have diminished growth in the absence of the nitrogen source. The transcriptome analysis of the A1S_1978 deletion mutant revealed that 253 genes were differentially expressed, including 80 genes that were upregulated by at least 2-fold and 173 genes that were down regulated in the ΔA1S_1978 strain. The transcriptome data showed an association between the A1S_1978 RR and key genes related to various nitrogen and amino acid metabolism processes, which was further confirmed by real time PCR analysis. The deletion of this RR leads to a reduction in persister cell formation against ciprofloxacin antibiotic. Taken together the results of this investigation provide significant evidence that the RR A1S_1978 is a global regulator in A. baumannii.
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Affiliation(s)
- Ajit Ramesh Sawant
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Sudhakar Pagal
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - K Prashanth
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, India.
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Trinchillo A, Valente V, Esposito M, Migliaccio M, Iovino A, Picciocchi M, Cuomo N, Caccavale C, Nocerino C, De Rosa L, Salvatore E, Pierantoni GM, Menchise V, Paladino S, Criscuolo C. Expanding SPG18 clinical spectrum: autosomal dominant mutation causes complicated hereditary spastic paraplegia in a large family. Neurol Sci 2024; 45:4373-4381. [PMID: 38607533 DOI: 10.1007/s10072-024-07500-0] [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: 01/15/2024] [Accepted: 03/21/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND SPG18 is caused by mutations in the endoplasmic reticulum lipid raft associated 2 (ERLIN2) gene. Autosomal recessive (AR) mutations are usually associated with complicated hereditary spastic paraplegia (HSP), while autosomal dominant (AD) mutations use to cause pure SPG18. AIM To define the variegate clinical spectrum of the SPG18 and to evaluate a dominant negative effect of erlin2 (encoded by ERLIN2) on oligomerization as causing differences between AR and AD phenotypes. METHODS In a four-generation pedigree with an AD pattern, a spastic paraplegia multigene panel test was performed. Oligomerization of erlin2 was analyzed with velocity gradient assay in fibroblasts of the proband and healthy subjects. RESULTS Despite the common p.V168M mutation identified in ERLIN2, a phenoconversion to amyotrophic lateral sclerosis (ALS) was observed in the second generation, pure HSP in the third generation, and a complicated form with psychomotor delay and epilepsy in the fourth generation. Erlin2 oligomerization was found to be normal. DISCUSSION We report the first AD SPG18 family with a complicated phenotype, and we ruled out a dominant negative effect of V168M on erlin2 oligomerization. Therefore, our data do not support the hypothesis of a relationship between the mode of inheritance and the phenotype, but confirm the multifaceted nature of SPG18 on both genetic and clinical point of view. Clinicians should be aware of the importance of conducting an in-depth clinical evaluation to unmask all the possible manifestations associated to an only apparently pure SPG18 phenotype. We confirm the genotype-phenotype correlation between V168M and ALS emphasizing the value of close follow-up.
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Affiliation(s)
- Assunta Trinchillo
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University Federico II of Naples, Naples, Italy
| | - Valeria Valente
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | | | | | - Aniello Iovino
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University Federico II of Naples, Naples, Italy
| | - Michele Picciocchi
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Nunzia Cuomo
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University Federico II of Naples, Naples, Italy
| | - Carmela Caccavale
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University Federico II of Naples, Naples, Italy
| | - Cristofaro Nocerino
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University Federico II of Naples, Naples, Italy
| | - Laura De Rosa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Elena Salvatore
- CDCD Neurology, "Federico II" University Hospital, Naples, Italy
| | - Giovanna Maria Pierantoni
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Valeria Menchise
- Institute of Biostructure and Bioimaging, National Research Council (CNR) and Molecular Biotechnology Center, Turin, Italy
| | - Simona Paladino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Chiara Criscuolo
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University Federico II of Naples, Naples, Italy.
- CDCD Neurology, "Federico II" University Hospital, Naples, Italy.
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Song H, Ni B, Peng X, Xu W, Yang S, Yang R, Wang Z, Li K, Lin R, Zhang Y, Guo J, Wu K, Shi G, Sun J, He C, Liu Y. MPZL1 as an HGF/MET signaling amplifier promotes cell migration and invasion in glioblastoma. Genes Dis 2024; 11:101085. [PMID: 38882007 PMCID: PMC11176650 DOI: 10.1016/j.gendis.2023.101085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/26/2023] [Accepted: 07/24/2023] [Indexed: 06/18/2024] Open
Affiliation(s)
- Haimin Song
- Department of Neurosurgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, China
| | - Bowen Ni
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan, Guangdong 528300, China
| | - Xuetao Peng
- Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan, Guangdong 528300, China
| | - Weijuan Xu
- Bidding and Procurement Office, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan, Guangdong 528300, China
| | - Shaochun Yang
- Department of Neurosurgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, China
| | - Runwei Yang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Ziyu Wang
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan, Guangdong 528300, China
| | - Kaishu Li
- Department of Neurosurgery, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, Guangdong 511518, China
| | - Rui Lin
- Department of Neurosurgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yunxiao Zhang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Jinglin Guo
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Kezhi Wu
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan, Guangdong 528300, China
| | - Guangwei Shi
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan, Guangdong 528300, China
| | - Jichao Sun
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 518020, China
| | - Chunming He
- Department of Neurosurgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, China
| | - Yawei Liu
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan, Guangdong 528300, China
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Kushwah AS, Dixit H, Upadhyay V, Verma SK, Prasad R. The study of iron- and copper-binding proteome of Fusarium oxysporum and its effector candidates. Proteins 2024; 92:1097-1112. [PMID: 38666709 DOI: 10.1002/prot.26696] [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: 07/05/2023] [Revised: 03/26/2024] [Accepted: 04/08/2024] [Indexed: 08/07/2024]
Abstract
Fusarium oxysporum f.sp. lycopersici is a phytopathogen which causes vascular wilt disease in tomato plants. The survival tactics of both pathogens and hosts depend on intricate interactions between host plants and pathogenic microbes. Iron-binding proteins (IBPs) and copper-binding proteins (CBPs) play a crucial role in these interactions by participating in enzyme reactions, virulence, metabolism, and transport processes. We employed high-throughput computational tools at the sequence and structural levels to investigate the IBPs and CBPs of F. oxysporum. A total of 124 IBPs and 37 CBPs were identified in the proteome of Fusarium. The ranking of amino acids based on their affinity for binding with iron is Glu > His> Asp > Asn > Cys, and for copper is His > Asp > Cys respectively. The functional annotation, determination of subcellular localization, and Gene Ontology analysis of these putative IBPs and CBPs have unveiled their potential involvement in a diverse array of cellular and biological processes. Three iron-binding glycosyl hydrolase family proteins, along with four CBPs with carbohydrate-binding domains, have been identified as potential effector candidates. These proteins are distinct from the host Solanum lycopersicum proteome. Moreover, they are known to be located extracellularly and function as enzymes that degrade the host cell wall during pathogen-host interactions. The insights gained from this report on the role of metal ions in plant-pathogen interactions can help develop a better understanding of their fundamental biology and control vascular wilt disease in tomato plants.
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Affiliation(s)
- Ankita Singh Kushwah
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Vipin Upadhyay
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Shailender Kumar Verma
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
- Department of Environmental Studies, University of Delhi, North Campus, Delhi, India
| | - Ramasare Prasad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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Abd-Hamid NA, Ismail I. An F-box Kelch repeat protein, PmFBK2, from Persicaria minor interacts with GID1b to modulate gibberellin signalling. JOURNAL OF PLANT PHYSIOLOGY 2024; 300:154299. [PMID: 38936241 DOI: 10.1016/j.jplph.2024.154299] [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: 10/26/2023] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024]
Abstract
The F-box protein (FBP) family plays diverse functions in the plant kingdom, with the function of many members still unrevealed. In this study, a specific FBP called PmFBK2, containing Kelch repeats from Persicaria minor, was functionally investigated. Employing the yeast two-hybrid (Y2H) assay, PmFBK2 was found to interact with Skp1-like proteins from P. minor, suggesting its potential to form an E3 ubiquitin ligase, known as the SCF complex. Y2H and co-immunoprecipitation tests revealed that PmFBK2 interacts with full-length PmGID1b. The interaction marks the first documented binding between these two protein types, which have never been reported in other plants before, and they exhibited a negative effect on gibberellin (GA) signal transduction. The overexpression of PmFBK2 in the kmd3 mutant, a homolog from Arabidopsis, demonstrated the ability of PmFBK2 to restore the function of the mutated KMD3 gene. The function restoration was supported by morphophysiological and gene expression analyses, which exhibited patterns similar to the wild type (WT) compared to the kmd3 mutant. Interestingly, the overexpression of PmFBK2 or PmGID1b in Arabidopsis had opposite effects on rosette diameter, seed weight, and plant height. This study provides new insights into the complex GA signalling. It highlights the crucial roles of the interaction between FBP and the GA receptor (GID1b) in regulating GA responses. These findings have implications for developing strategies to enhance plant growth and yield by modulating GA signalling in crops.
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Affiliation(s)
- Nur-Athirah Abd-Hamid
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia; Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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Almeida GMDF, Ravantti J, Grdzelishvili N, Kakabadze E, Bakuradze N, Javakhishvili E, Megremis S, Chanishvili N, Papadopoulos N, Sundberg LR. Relevance of the bacteriophage adherence to mucus model for Pseudomonas aeruginosa phages. Microbiol Spectr 2024; 12:e0352023. [PMID: 38912817 PMCID: PMC11302309 DOI: 10.1128/spectrum.03520-23] [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: 09/29/2023] [Accepted: 05/13/2024] [Indexed: 06/25/2024] Open
Abstract
Pseudomonas aeruginosa infections are getting increasingly serious as antimicrobial resistance spreads. Phage therapy may be a solution to the problem, especially if improved by current advances on phage-host studies. As a mucosal pathogen, we hypothesize that P. aeruginosa and its phages are linked to the bacteriophage adherence to mucus (BAM) model. This means that phage-host interactions could be influenced by mucin presence, impacting the success of phage infections on the P. aeruginosa host and consequently leading to the protection of the metazoan host. By using a group of four different phages, we tested three important phenotypes associated with the BAM model: phage binding to mucin, phage growth in mucin-exposed hosts, and the influence of mucin on CRISPR immunity of the bacterium. Three of the tested phages significantly bound to mucin, while two had improved growth rates in mucin-exposed hosts. Improved phage growth was likely the result of phage exploitation of mucin-induced physiological changes in the host. We could not detect CRISPR activity in our system but identified two putative anti-CRISPR proteins coded by the phage. Overall, the differential responses seen for the phages tested show that the same bacterial species can be targeted by mucosal-associated phages or by phages not affected by mucus presence. In conclusion, the BAM model is relevant for phage-bacterium interactions in P. aeruginosa, opening new possibilities to improve phage therapy against this important pathogen by considering mucosal interaction dynamics.IMPORTANCESome bacteriophages are involved in a symbiotic relationship with animals, in which phages held in mucosal surfaces protect them from invading bacteria. Pseudomonas aeruginosa is one of the many bacterial pathogens threatening humankind during the current antimicrobial resistance crisis. Here, we have tested whether P. aeruginosa and its phages are affected by mucosal conditions. We discovered by using a collection of four phages that, indeed, mucosal interaction dynamics can be seen in this model. Three of the tested phages significantly bound to mucin, while two had improved growth rates in mucin-exposed hosts. These results link P. aeruginosa and its phages to the bacteriophage adherence to the mucus model and open opportunities to explore this to improve phage therapy, be it by exploiting the phenotypes detected or by actively selecting mucosal-adapted phages for treatment.
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Affiliation(s)
- Gabriel Magno de Freitas Almeida
- Faculty of Biosciences, Fisheries and Economics, The Norwegian College of Fishery Science, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Janne Ravantti
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Nino Grdzelishvili
- George Eliava Institute of Bacteriophages, Microbiology & Virology, Tbilisi, Georgia
- Faculty of Natural Science and Medicine, Ilia State University, Tbilisi, Georgia
| | - Elene Kakabadze
- George Eliava Institute of Bacteriophages, Microbiology & Virology, Tbilisi, Georgia
| | - Nata Bakuradze
- George Eliava Institute of Bacteriophages, Microbiology & Virology, Tbilisi, Georgia
| | - Elene Javakhishvili
- George Eliava Institute of Bacteriophages, Microbiology & Virology, Tbilisi, Georgia
| | | | - Nina Chanishvili
- George Eliava Institute of Bacteriophages, Microbiology & Virology, Tbilisi, Georgia
| | | | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science and Nanoscience Centre, University of Jyväskylä, Jyväskylä, Finland
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11
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Ma J, Yang L, Dang Y, Shahzad K, Song J, Jia B, Wang L, Feng J, Wang N, Pei W, Wu M, Zhang X, Zhang J, Wu J, Yu J. Deciphering the dynamic expression network of fiber elongation and the functional role of the GhTUB5 gene for fiber length in cotton based on an introgression population of upland cotton. J Adv Res 2024:S2090-1232(24)00324-2. [PMID: 39106927 DOI: 10.1016/j.jare.2024.08.004] [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: 02/27/2024] [Revised: 07/02/2024] [Accepted: 08/02/2024] [Indexed: 08/09/2024] Open
Abstract
INTRODUCTION Interspecific introgression between Gossypium hirsutum and G. barbadense allows breeding cotton with outstanding fiber length (FL). However, the dynamic gene regulatory network of FL-related genes has not been characterized, and the functional mechanism through which the hub gene GhTUB5 mediates fiber elongation has yet to be determined. METHODS Coexpression analyses of 277 developing fiber transcriptomes integrated with QTL mapping using 250 introgression lines of different FL phenotypes were conducted to identify genes related to fiber elongation. The function of GhTUB5 was determined by ectopic expression of two TUB5 alleles in Arabidopsis and knockout of GhTUB5 in upland cotton. Yeast two-hybrid, split-luciferase and pull-down assays were conducted to screen for interacting proteins, and upstream genes were identified by yeast one-hybrid, dual-LUC and electrophoretic mobility shift assays. RESULTS The 32,612, 30,837 and 30,277 genes expressed at 5, 10 and 15 days postanthesis (dpa) were grouped into 19 distinct coexpression modules, and 988 genes in the MEblack module were enriched in the cell wall process and exhibited significant associations with FL. A total of 20 FL-QTLs were identified, each explaining 3.34-16.04 % of the phenotypic variance in the FL. Furthermore, several FL-QTLs contained 15 genes that were differentially expressed in the MEblack module including the tubulin beta gene (TUB5). Compared with the wild type, the overexpression of GhTUB5 and GbTUB5 in Arabidopsis suppressed root cell length but promoted cellulose synthesis. Knockout of GhTUB5 resulted in longer fiber lines. Protein-based experiments revealed that GhTUB5 interacts with GhZFP6. Additionally, GhTUB5 was directly activated by GhHD-ZIP7, a homeobox-leucine zipper transcription factor, and its paralogous gene was previously reported to mediate fiber elongation. CONCLUSION This study opens a new avenue to dissect functional mechanism of cotton fiber elongation. Our findings provide some molecular details on how GhTUB5 mediates the FL phenotype in cotton.
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Affiliation(s)
- Jianjiang Ma
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Liupeng Yang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yuanyue Dang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China
| | - Kashif Shahzad
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jikun Song
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bing Jia
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Li Wang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Juanjuan Feng
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Nuohan Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Man Wu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Xuexian Zhang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, USA.
| | - Jianyong Wu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.
| | - Jiwen Yu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China; Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China.
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12
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Liu T, Liu H, Xian W, Liu Z, Yuan Y, Fan J, Xiang S, Yang X, Liu Y, Liu S, Zhang M, Shen Y, Jiao Y, Cheng S, Doyle JJ, Xie F, Li J, Tian Z. Duplication and sub-functionalization of flavonoid biosynthesis genes plays important role in Leguminosae root nodule symbiosis evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 39092779 DOI: 10.1111/jipb.13743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 08/04/2024]
Abstract
Gene innovation plays an essential role in trait evolution. Rhizobial symbioses, the most important N2-fixing agent in agricultural systems that exists mainly in Leguminosae, is one of the most attractive evolution events. However, the gene innovations underlying Leguminosae root nodule symbiosis (RNS) remain largely unknown. Here, we investigated the gene gain event in Leguminosae RNS evolution through comprehensive phylogenomic analyses. We revealed that Leguminosae-gain genes were acquired by gene duplication and underwent a strong purifying selection. Kyoto Encyclopedia of Genes and Genomes analyses showed that the innovated genes were enriched in flavonoid biosynthesis pathways, particular downstream of chalcone synthase (CHS). Among them, Leguminosae-gain type Ⅱ chalcone isomerase (CHI) could be further divided into CHI1A and CHI1B clades, which resulted from the products of tandem duplication. Furthermore, the duplicated CHI genes exhibited exon-intron structural divergences evolved through exon/intron gain/loss and insertion/deletion. Knocking down CHI1B significantly reduced nodulation in Glycine max (soybean) and Medicago truncatula; whereas, knocking down its duplication gene CHI1A had no effect on nodulation. Therefore, Leguminosae-gain type Ⅱ CHI participated in RNS and the duplicated CHI1A and CHI1B genes exhibited RNS functional divergence. This study provides functional insights into Leguminosae-gain genetic innovation and sub-functionalization after gene duplication that contribute to the evolution and adaptation of RNS in Leguminosae.
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Affiliation(s)
- Tengfei Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiyue Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wenfei Xian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
| | - Zhi Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Hebei Key Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shi-jiazhuang, 050035, China
| | - Yaqin Yuan
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingwei Fan
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuaiying Xiang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xia Yang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yucheng Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shulin Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Min Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanting Shen
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuannian Jiao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Jeff J Doyle
- School of Integrative Plant Science, Sections of Plant Biology and Plant Breeding & Genetics, Cornell University, Ithaca, 14853, New York, USA
| | - Fang Xie
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jiayang Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Yazhouwan National Laboratory, Sanya, 572024, China
| | - Zhixi Tian
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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13
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Saghour N, Chérifi F, Saoud S, Zebbiche Y, Meribai A, Bekkari N, Samya TM, Laraba-Djebari F. Structural, Biochemical Characterization and Molecular Mechanism of Cerastokunin: A New Kunitz-Type Peptide with Potential Inhibition of Thrombin, Factor Xa and Platelets. Protein J 2024:10.1007/s10930-024-10226-9. [PMID: 39095592 DOI: 10.1007/s10930-024-10226-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2024] [Indexed: 08/04/2024]
Abstract
The current investigation focused on separating Cerastes cerastes venom to produce the first Kunitz-type peptide. Based on its anti-trypsin effect, Cerastokunin, a 7.75 kDa peptide, was purified until homogenity by three steps of chromatography. Cerastokunin was found to include 67 amino acid residues that were obtained by de novo sequencing using LC-MALDI-MSMS. Upon alignment with Kunitz-type peptides, there was a high degree of similarity. Cerastokunin's 3D structure had 12% α-helices and 21% β-strands with pI 8.48. Cerastokunin showed a potent anticoagulant effect by inhibiting the protease activity of thrombin and trypsin as well as blocking the intrinsic and extrinsic coagulation pathways. In both PT and aPPT, Cerastokunin increased the blood clotting time in a dose-dependent way. Using Lys48 and Gln192 for direct binding, Cerastokunin inhibited thrombin, Factor Xa and trypsin as shown by molecular docking. Cerastokunin exhibited a dose-response blockade of PARs-dependent pathway platelet once stimulated by thrombin. An increased concentration of Cerastokunin resulted in a larger decrease of tail thrombus in the mice-carrageenan model in an in vivo investigation when compared to the effects of antithrombotic medications. At all Cerastokunin doses up to 6 mg/kg, no in vivo toxicity was seen in challenged mice over the trial's duration.
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Affiliation(s)
- Noussaiba Saghour
- Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, USTHB, BP 32 El-Alia, Bab Ezzouar, Algiers, Algeria
| | - Fatah Chérifi
- Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, USTHB, BP 32 El-Alia, Bab Ezzouar, Algiers, Algeria.
| | - Samah Saoud
- Faculty of Sciences, University of Algiers 1, Algiers, Algeria
| | - Younes Zebbiche
- Faculty of Pharmacy, University of Algiers 1, Algiers, Algeria
| | - Amel Meribai
- Food Technology and Human Nutrition Research Laboratory, National Agronomic High School, Algiers, Algeria
| | - Nadjia Bekkari
- Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, USTHB, BP 32 El-Alia, Bab Ezzouar, Algiers, Algeria
| | | | - Fatima Laraba-Djebari
- Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, USTHB, BP 32 El-Alia, Bab Ezzouar, Algiers, Algeria
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14
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Velasco‐Carneros L, Bernardo‐Seisdedos G, Maréchal J, Millet O, Moro F, Muga A. Pseudophosphorylation of single residues of the J-domain of DNAJA2 regulates the holding/folding balance of the Hsc70 system. Protein Sci 2024; 33:e5105. [PMID: 39012012 PMCID: PMC11249846 DOI: 10.1002/pro.5105] [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: 03/14/2024] [Revised: 06/20/2024] [Accepted: 06/23/2024] [Indexed: 07/17/2024]
Abstract
The Hsp70 system is essential for maintaining protein homeostasis and comprises a central Hsp70 and two accessory proteins that belong to the J-domain protein (JDP) and nucleotide exchange factor families. Posttranslational modifications offer a means to tune the activity of the system. We explore how phosphorylation of specific residues of the J-domain of DNAJA2, a class A JDP, regulates Hsc70 activity using biochemical and structural approaches. Among these residues, we find that pseudophosphorylation of Y10 and S51 enhances the holding/folding balance of the Hsp70 system, reducing cochaperone collaboration with Hsc70 while maintaining the holding capacity. Truly phosphorylated J domains corroborate phosphomimetic variant effects. Notably, distinct mechanisms underlie functional impacts of these DNAJA2 variants. Pseudophosphorylation of Y10 induces partial disordering of the J domain, whereas the S51E substitution weakens essential DNAJA2-Hsc70 interactions without a large structural reorganization of the protein. S51 phosphorylation might be class-specific, as all cytosolic class A human JDPs harbor a phosphorylatable residue at this position.
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Affiliation(s)
- Lorea Velasco‐Carneros
- Instituto Biofisika (UPV/EHU, CSIC)University of Basque CountryLeioaSpain
- Department of Biochemistry and Molecular Biology, Faculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
| | - Ganeko Bernardo‐Seisdedos
- Precision Medicine and Metabolism LabCIC bioGUNEDerioSpain
- Department of Medicine, Faculty of Health SciencesUniversity of DeustoBilbaoSpain
| | - Jean‐Didier Maréchal
- Insilichem, Departament de QuímicaUniversitat Autònoma de Barcelona (UAB)Bellaterra (Barcelona)Spain
| | - Oscar Millet
- Precision Medicine and Metabolism LabCIC bioGUNEDerioSpain
| | - Fernando Moro
- Instituto Biofisika (UPV/EHU, CSIC)University of Basque CountryLeioaSpain
- Department of Biochemistry and Molecular Biology, Faculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
| | - Arturo Muga
- Instituto Biofisika (UPV/EHU, CSIC)University of Basque CountryLeioaSpain
- Department of Biochemistry and Molecular Biology, Faculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
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15
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Aiman S, Ali Y, Malik A, Alkholief M, Ahmad A, Akhtar S, Ali S, Khan A, Li C, Shams S. Immunoinformatic-guided novel mRNA vaccine designing to elicit immunogenic responses against the endemic Monkeypox virus. J Biomol Struct Dyn 2024; 42:6292-6306. [PMID: 37424185 DOI: 10.1080/07391102.2023.2233627] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
Monkeypox virus (MPXV) is an orthopoxvirus, causing zoonotic infections in humans with smallpox-like symptoms. The WHO reported MPXV cases in May 2022 and the outbreak caused significant morbidity threats to immunocompromised individuals and children. Currently, no clinically validated therapies are available against MPXV infections. The present study is based on immunoinformatics approaches to design mRNA-based novel vaccine models against MPXV. Three proteins were prioritized based on high antigenicity, low allergenicity, and toxicity values to predict T- and B-cell epitopes. Lead T- and B-cell epitopes were used to design vaccine constructs, linked with epitope-specific linkers and adjuvant to enhance immune responses. Additional sequences, including Kozak sequence, MITD sequence, tPA sequence, Goblin 5', 3' UTRs, and a poly(A) tail were added to design stable and highly immunogenic mRNA vaccine construct. High-quality structures were predicted by molecular modeling and 3D-structural validation of the vaccine construct. Population coverage and epitope-conservancy speculated broader protection of designed vaccine model against multiple MPXV infectious strains. MPXV-V4 was eventually prioritized based on its physicochemical and immunological parameters and docking scores. Molecular dynamics and immune simulations analyses predicted significant structural stability and binding affinity of the top-ranked vaccine model with immune receptors to elicit cellular and humoral immunogenic responses against the MPXV. The pursuance of experimental and clinical follow-up of these prioritized constructs may lay the groundwork to develop safe and effective vaccine against MPXV.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Yasir Ali
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Musaed Alkholief
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abbas Ahmad
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Suhail Akhtar
- A.T. Still University of Health Sciences, Kirksville, MO, USA
| | - Sajid Ali
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
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Su B, Yang W, Zhou Y, Lin J. Efficiently manufacturing ectoine via metabolic engineering and protein engineering of L-2,4-diaminobutyrate transaminase. Int J Biol Macromol 2024; 275:133612. [PMID: 38960226 DOI: 10.1016/j.ijbiomac.2024.133612] [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: 04/26/2024] [Revised: 06/16/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024]
Abstract
Ectoine, so-called tetrahydropyrimidine, is an important osmotic adjustment solute and widely applied in cosmetics and protein protectant. Some attempts have been made to improve the ectoine productivity. However, the strains with both high ectoine production capacity and high glucose conversion were still absent so far. Aim to construct a strain for efficiently producing ectoine, ectoine synthetic gene cluster ectABC from Pseudomonas stutzeri was overexpressed in E. coli BL21 (DE3). The ection production was improved by 382 % (ectoine titer increased from 1.73 g/L to 8.33 g/L) after the rational design of rate-limiting enzyme L-2,4-diaminobutyrate transaminase EctBps (protein engineering) combined with the metabolic engineering that focused on the enrichment and conversion of precursors. The final strain YW20 was applied to overproduce ectoine in fed-batch fermentation and yield 68.9 g/L of ectoine with 0.88 g/L/h of space-time yield and the highest glucose conversion reported [34 % (g/g)]. From the fermentation broth, ectoine was purified with 99.7 % purity and 79.8 % yield. This study successfully provided an engineered strain as well as an efficient method for the industrial bio-synthesis and preparation of ectoine.
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Affiliation(s)
- Bingmei Su
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Institute of Enzyme Catalysis and Synthetic Biotechnology, Fuzhou University, Fuzhou 350108, China
| | - Wen Yang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Yi Zhou
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Juan Lin
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Institute of Enzyme Catalysis and Synthetic Biotechnology, Fuzhou University, Fuzhou 350108, China.
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17
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Burgardt NI, Melian NA, González Flecha FL. Copper resistance in the cold: Genome analysis and characterisation of a P IB-1 ATPase in Bizionia argentinensis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13278. [PMID: 38943264 PMCID: PMC11213822 DOI: 10.1111/1758-2229.13278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/19/2024] [Indexed: 07/01/2024]
Abstract
Copper homeostasis is a fundamental process in organisms, characterised by unique pathways that have evolved to meet specific needs while preserving core resistance mechanisms. While these systems are well-documented in model bacteria, information on copper resistance in species adapted to cold environments is scarce. This study investigates the potential genes related to copper homeostasis in the genome of Bizionia argentinensis (JUB59-T), a psychrotolerant bacterium isolated from Antarctic seawater. We identified several genes encoding proteins analogous to those crucial for copper homeostasis, including three sequences of copper-transport P1B-type ATPases. One of these, referred to as BaCopA1, was chosen for cloning and expression in Saccharomyces cerevisiae. BaCopA1 was successfully integrated into yeast membranes and subsequently extracted with detergent. The purified BaCopA1 demonstrated the ability to catalyse ATP hydrolysis at low temperatures. Structural models of various BaCopA1 conformations were generated and compared with mesophilic and thermophilic homologous structures. The significant conservation of critical residues and structural similarity among these proteins suggest a shared reaction mechanism for copper transport. This study is the first to report a psychrotolerant P1B-ATPase that has been expressed and purified in a functional form.
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Affiliation(s)
- Noelia I. Burgardt
- Laboratorio de Biofísica Molecular, Facultad de Farmacia y Bioquímica, Instituto de Química y Fisicoquímica BiológicasUniversidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y TécnicasBuenos AiresArgentina
- Present address:
Departamento de Ciencia y TecnologíaUniversidad Nacional de QuilmesBernalArgentina
| | - Noelia A. Melian
- Laboratorio de Biofísica Molecular, Facultad de Farmacia y Bioquímica, Instituto de Química y Fisicoquímica BiológicasUniversidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y TécnicasBuenos AiresArgentina
| | - F. Luis González Flecha
- Laboratorio de Biofísica Molecular, Facultad de Farmacia y Bioquímica, Instituto de Química y Fisicoquímica BiológicasUniversidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y TécnicasBuenos AiresArgentina
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18
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Wang Q, Phang JM, Chakraborty S, Zhang L, Klähn M, Nalaparaju A, Lim FCH. Atomistic Characterization of Healthy and Damaged Hair Surfaces: A Molecular Dynamics Simulation Study of Fatty Acids on Protein Layer. Chembiochem 2024; 25:e202400128. [PMID: 38842537 DOI: 10.1002/cbic.202400128] [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: 02/10/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/07/2024]
Abstract
Amid the bourgeoning demand for in-silico designed, environmentally sustainable, and highly effective hair care formulations, a growing interest is evident in the exploration of realistic computational model for the hair surface. In this work, we present an atomistic model for the outermost layer of the hair surface derived through molecular dynamics simulations, which comprises 18-Methyleicosanoic acid (18-MEA) fatty acid chains covalently bound onto the keratin-associated protein 10-4 (KAP10-4) at a spacing distance of ~1 nm. Remarkably, this hair surface model facilitates the inclusion of free fatty acids (free 18-MEA) into the gaps between chemically bound 18-MEA chains, up to a maximum number that results in a packing density of 0.22 nm2 per fatty acid molecule, consistent with the optimal spacing identified through free energy analysis. Atomistic insights are provided for the organization of fatty acid chains, structural features, and interaction energies on protein-inclusive hair surface models with varying amounts of free 18-MEA (FMEA) depletion, as well as varying degrees of anionic cysteic acid from damaged bound 18-MEA (BMEA), under both dry and wet conditions. In the presence of FMEA and water, the fatty acid chains in a pristine hair surface prefers to adopt a thermodynamically favored extended chain conformation, forming a thicker protective layer (~3 nm) on the protein surface. Our simulation results reveal that, while the depletion of FMEA can induce a pronounced impact on the thickness, tilt angle, and order parameters of fatty acid chains, the removal of BMEA has a marked effect on water penetration. There is a "sweet spot" spacing between the 18-MEA whereby damaged hair surface properties can be reinstated by replenishing FMEA. Through the incorporation of the protein layer and free fatty acids, the hair surface models presented in this study enables a realistic representation of the intricate details within the hair epicuticle, facilitating a molecular scale assessment of surface properties during the formulation design process.
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Affiliation(s)
- Qiang Wang
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis North, Singapore, 138632, Republic of Singapore
| | - Jia Min Phang
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis North, Singapore, 138632, Republic of Singapore
| | - Souvik Chakraborty
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis North, Singapore, 138632, Republic of Singapore
| | - Liling Zhang
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis North, Singapore, 138632, Republic of Singapore
| | - Marco Klähn
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis North, Singapore, 138632, Republic of Singapore
- Current address: AstraZeneca, Pepparedsleden 1, SE-431 83, Mölndal, Sweden
| | - Anjaiah Nalaparaju
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis North, Singapore, 138632, Republic of Singapore
| | - Freda C H Lim
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis North, Singapore, 138632, Republic of Singapore
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19
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Kumar H, Kim P. Artificial intelligence in fusion protein three-dimensional structure prediction: Review and perspective. Clin Transl Med 2024; 14:e1789. [PMID: 39090739 PMCID: PMC11294035 DOI: 10.1002/ctm2.1789] [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: 03/22/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 08/04/2024] Open
Abstract
Recent advancements in artificial intelligence (AI) have accelerated the prediction of unknown protein structures. However, accurately predicting the three-dimensional (3D) structures of fusion proteins remains a difficult task because the current AI-based protein structure predictions are focused on the WT proteins rather than on the newly fused proteins in nature. Following the central dogma of biology, fusion proteins are translated from fusion transcripts, which are made by transcribing the fusion genes between two different loci through the chromosomal rearrangements in cancer. Accurately predicting the 3D structures of fusion proteins is important for understanding the functional roles and mechanisms of action of new chimeric proteins. However, predicting their 3D structure using a template-based model is challenging because known template structures are often unavailable in databases. Deep learning (DL) models that utilize multi-level protein information have revolutionized the prediction of protein 3D structures. In this review paper, we highlighted the latest advancements and ongoing challenges in predicting the 3D structure of fusion proteins using DL models. We aim to explore both the advantages and challenges of employing AlphaFold2, RoseTTAFold, tr-Rosetta and D-I-TASSER for modelling the 3D structures. HIGHLIGHTS: This review provides the overall pipeline and landscape of the prediction of the 3D structure of fusion protein. This review provides the factors that should be considered in predicting the 3D structures of fusion proteins using AI approaches in each step. This review highlights the latest advancements and ongoing challenges in predicting the 3D structure of fusion proteins using deep learning models. This review explores the advantages and challenges of employing AlphaFold2, RoseTTAFold, tr-Rosetta, and D-I-TASSER to model 3D structures.
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Affiliation(s)
- Himansu Kumar
- Department of Bioinformatics and Systems MedicineMcWilliams School of Biomedical InformaticsThe University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Pora Kim
- Department of Bioinformatics and Systems MedicineMcWilliams School of Biomedical InformaticsThe University of Texas Health Science Center at HoustonHoustonTexasUSA
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20
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Paineau M, Minio A, Mestre P, Fabre F, Mazet ID, Couture C, Legeai F, Dumartinet T, Cantu D, Delmotte F. Multiple deletions of candidate effector genes lead to the breakdown of partial grapevine resistance to downy mildew. THE NEW PHYTOLOGIST 2024; 243:1490-1505. [PMID: 39021210 DOI: 10.1111/nph.19861] [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: 10/17/2023] [Accepted: 03/21/2024] [Indexed: 07/20/2024]
Abstract
Grapevine downy mildew, caused by the oomycete Plasmopara viticola (P. viticola, Berk. & M. A. Curtis; Berl. & De Toni), is a global threat to Eurasian wine grapes Vitis vinifera. Although resistant grapevine varieties are becoming more accessible, P. viticola populations are rapidly evolving to overcome these resistances. We aimed to uncover avirulence genes related to Rpv3.1-mediated grapevine resistance. We sequenced the genomes and characterized the development of 136 P. viticola strains on resistant and sensitive grapevine cultivars. A genome-wide association study was conducted to identify genomic variations associated with resistant-breaking phenotypes. We identified a genomic region associated with the breakdown of Rpv3.1 grapevine resistance (avrRpv3.1 locus). A diploid-aware reassembly of the P. viticola INRA-Pv221 genome revealed structural variations in this locus, including a 30 kbp deletion. Virulent P. viticola strains displayed multiple deletions on both haplotypes at the avrRpv3.1 locus. These deletions involve two paralog genes coding for proteins with 800-900 amino acids and signal peptides. These proteins exhibited a structure featuring LWY-fold structural modules, common among oomycete effectors. When transiently expressed, these proteins induced cell death in grapevines carrying Rpv3.1 resistance, confirming their avirulence nature. This discovery sheds light on the genetic mechanisms enabling P. viticola to adapt to grapevine resistance, laying a foundation for developing strategies to manage this destructive crop pathogen.
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Affiliation(s)
- Manon Paineau
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
- Department of Viticulture and Enology, University of California Davis, Davis, 95616, CA, USA
| | - Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis, 95616, CA, USA
| | - Pere Mestre
- INRAE, Université de Strasbourg, SVQV, F-68125, Colmar, France
| | - Frédéric Fabre
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
| | - Isabelle D Mazet
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
| | - Carole Couture
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
| | - Fabrice Legeai
- INRAE, IGEPP, F-35650, Le-Rheu, France
- INRIA, IRISA, GenOuest Core Facility, F-35000, Rennes, France
| | | | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, 95616, CA, USA
- Genome Center, University of California Davis, Davis, 95616, CA, USA
| | - François Delmotte
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
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21
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Kamal MM, Islam MN, Rabby MG, Zahid MA, Hasan MM. In Silico Functional and Structural Analysis of Non-synonymous Single Nucleotide Polymorphisms (nsSNPs) in Human Paired Box 4 Gene. Biochem Genet 2024; 62:2975-2998. [PMID: 38062275 DOI: 10.1007/s10528-023-10589-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 11/06/2023] [Indexed: 07/31/2024]
Abstract
In human genome, members of Paired box (PAX) transcription factor family are highly sequence-specific DNA-binding proteins. Among PAX gene family members, PAX4 gene has significant role in growth, proliferation, differentiation, and insulin secretion of pancreatic β-cells. Single nucleotide polymorphisms (SNPs) in PAX4 gene progress in the pathogenesis of various human diseases. Hence, the molecular mechanism of how these SNPs in PAX4 gene significantly progress diseases pathogenesis needs to be elucidated. For the reason, a series of bioinformatic analyzes were done to identify the SNPs of PAX4 gene that contribute in diseases pathogenesis. From the analyzes, 4145 SNPs (rsIDs) in PAX4 gene were obtained, where, 362 missense (8.73%), 169 synonymous (4.08%), and 2323 intron variants (56.04%). The rest SNPs were unspecified. Among the 362 missense variants, 118 nsSNPs were found as deleterious in SIFT analysis. Among those, 25 nsSNPs were most probably damaging and 23 were deleterious as observed in PolyPhen-2 and PROVEAN analyzes, respectively. Following all analyzes, 14 nsSNPs (rs149708455, rs115887120, rs147279315, rs35155575, rs370095957, rs373939873, rs145468905, rs121917718, rs2233580, rs3824004, rs372751660, rs369459316, rs375472849, rs372497946) were common and observed as deleterious, probably damaging, affective and diseases associated. Following structural analyzes, 11 nsSNPs guided proteins were found as most unstable and highly conserved. Among these, R20W, R39Q, R45Q, R60H, G65D, and A223D mutated proteins were highly harmful. Hence, the results from above-mentioned integrated comprehensive bioinformatic analyzes guide how different nsSNPs in PAX4 gene alter structural and functional characteristics of the protein that might progress diseases pathogenesis in human including type 2 diabetes.
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Affiliation(s)
- Md Mostafa Kamal
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Numan Islam
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh
- Department of Food Engineering, North Pacific International University of Bangladesh, Dhaka, Bangladesh
| | - Md Golam Rabby
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Ashrafuzzaman Zahid
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Mahmudul Hasan
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh.
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22
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Sharma S, Arpita K, Nirgude M, Srivastava H, Kumar K, Sreevathsa R, Bhattacharya R, Gaikwad K. Genomic insights into cytokinin oxidase/dehydrogenase (CKX) gene family, identification, phylogeny and synteny analysis for its possible role in regulating seed number in Pigeonpea (Cajanus cajan). Int J Biol Macromol 2024:134194. [PMID: 39097061 DOI: 10.1016/j.ijbiomac.2024.134194] [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: 04/29/2024] [Revised: 06/28/2024] [Accepted: 07/25/2024] [Indexed: 08/05/2024]
Abstract
Cytokinin oxidase/dehydrogenase (CKX) regulates cytokinin levels in plants which are vital for plant growth and development. However, there is a paucity of evidence regarding their role in controlling embryo/seed development in pigeonpea. This study is perhaps the first to provide information on the identification and characterization of CKX genes in pigeonpea. A genome-wide analysis identified 18 CKX genes, each with distinct structure, expression patterns, and possible diverse functions. Domain analysis revealed the presence of the sequences including FAD and CK-Binding domain, and subcellular localization analysis showed that almost 50 % of them reside within the nucleus. They were observed to be located unevenly on chromosome numbers 2, 4, 6, 7, and 11 with a majority of them present on the scaffold. The 8 homologous pairs and various orthologous gene pairs provided further insights into their evolution pattern. Further, SNP/Indels variation in CKX genes and haplotype groups among contrasting genotypes for SNPP (seed number per pod) were analyzed. Spatiotemporal expression analysis revealed the significant expression pattern of CcCKX15, CcCKX17, and CcCKX2 in genotypes carrying low SNPP reiterating their role as negative regulators. These genes can be potential targets to undertake crop improvement programs in pigeonpea.
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Affiliation(s)
- Sandhya Sharma
- National Institute for plant Biotechnology, New Delhi 110012, India.
| | - Kumari Arpita
- National Institute for plant Biotechnology, New Delhi 110012, India
| | | | | | - Kuldeep Kumar
- National Institute for plant Biotechnology, New Delhi 110012, India
| | | | | | - Kishor Gaikwad
- National Institute for plant Biotechnology, New Delhi 110012, India.
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23
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Bojórquez-Sánchez AM, Diaz-Vidal T, Rosales-Rivera LC, Leyva-Soto LA, Martínez-Alarcón D, Díaz-Tenorio LM, Martínez-Pérez RB. A contribution to lipid digestion of Odobenidae family: Computational analysis of gastric and pancreatic lipases from walrus (Odobenus rosmarus divergens). Int J Biol Macromol 2024; 275:132985. [PMID: 38871103 DOI: 10.1016/j.ijbiomac.2024.132985] [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: 09/16/2023] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024]
Abstract
Triacylglycerols (TAGs) are a primary energy source for marine mammals during lipid digestion. Walruses (Odobenus rosmarus divergens) consume prey with a high content of long-chain polyunsaturated fatty acids; however, their digestive physiology and lipid digestion remain poorly studied. The present study aims to model and characterize the gastric (PWGL) and pancreatic (PWPL) lipases of Pacific walruses using an in-silico approach. The confident 3D models of PWGL and PWPL were obtained via homology modeling and protein threading and displayed the structural features of lipases. Molecular docking analysis demonstrated substrate selectivity for long-chain TAG (Trieicosapentaenoin; TC20:5n-3) in PWGL and short-chain TAG (Trioctanoin; TC8:0) in PWPL. Molecular dynamics simulations demonstrate that PWGL bound to tridocosahexaenoin (TC22:6n-3), the protein is considerably stable at all three salinity conditions, but fluctuations are observed in the regions associated with catalytic sites and the lid, indicating the potential hydrolysis of the substrate. This is the first study to report on the digestion of TAGs in walruses, including modeling and lipases characterization and proposing a digestive tract for pinnipeds.
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Affiliation(s)
- Ana María Bojórquez-Sánchez
- Department of Biotechnology and Food Sciences, Instituto Tecnológico de Sonora, 85137 Ciudad Obregón, Mexico
| | - Tania Diaz-Vidal
- Department of Chemical Engineering, CUCEI, Universidad de Guadalajara, Guadalajara 44430, Mexico
| | | | - Luis Alonso Leyva-Soto
- Department of Biotechnology and Food Sciences, Instituto Tecnológico de Sonora, 85137 Ciudad Obregón, Mexico; CONAHCYT Chair Program, Researchers for México, Av. Insurgentes Sur 1582, Col Crédito Constructor Demarcación Territorial Benito Juárez, 03940 Ciudad de México, Mexico
| | - Diana Martínez-Alarcón
- UMR-MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Place Eugène Bataillon, Montpellier 34095, France
| | | | - Raúl Balam Martínez-Pérez
- Department of Biotechnology and Food Sciences, Instituto Tecnológico de Sonora, 85137 Ciudad Obregón, Mexico.
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24
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Yamchi A, Rahimi M, Akbari R, Ghobadi C, Aryapour H. Effects of Bacillus in Pectobacterium quorum quenching: A survey of two different acyl-homoserine lactonases. Folia Microbiol (Praha) 2024; 69:913-926. [PMID: 38305961 DOI: 10.1007/s12223-024-01139-2] [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: 08/08/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024]
Abstract
Numerous functions in pathogenic Pectobacterium are regulated by quorum sensing (QS). Two different aiiA genes isolated from Bacillus sp. A24(aiiAA24) and Bacillus sp. DMS133(aiiADMS133) were used. Both genes encode acyl-homoserine lactonase (AiiA), which disrupts QS in Pectobacterium. To investigate the effect of different AiiAs on the inhibition of Pectobacterium carotovorum pathogenicity, two aiiA genes from different Bacillus strains were cloned and the resulting plasmids pME6863 (aiiAA24) and pME7080 (aiiADMS133) were transformed into P. carotovorum EMPCC cells. The effects of different lactonases on virulence features such as enzymatic activity, twitching and swimming motilities, and production of pellicle and biofilm formation were investigated. In EMPCC/pME6863, twitching and swimming motilities, and pellicle production were significantly reduced compared with EMPCC/pME7080. Quantitative real-time PCR (qRT-PCR) was used to measure virulence gene expression in transformed cells compared with expression levels in wild-type EMPCC. The expression of peh and hrpL genes was greatly reduced in EMPCC/pME6863 compared with EMPCC/pME7080. The sequence alignment and molecular dynamic modeling of two different AiiAA24 and AiiADMS133 proteins suggested that the replacement of proline 210 from AiiAA24 to serine in AiiADMS133 caused the reduction of enzyme activity in AiiADMS133.
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Affiliation(s)
- Ahad Yamchi
- Department of Plant Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran.
| | - Maryam Rahimi
- Department of Horticulture, University of Zabol, Zabol, Iran
| | - Ramin Akbari
- Department of Agricultural Biotechnology, Isfahan University of Technology, Isfahan, Iran
| | - Cyrus Ghobadi
- Department of Horticulture Sciences, Isfahan University of Technology, Isfahan, Iran
| | - Hassan Aryapour
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran
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25
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Yang HW, Kim YW, Villafani Y, Song JY, Park YI. Teal-light absorbing cyanobacterial phytochrome superfamily provides insights into the diverse mechanisms of spectral tuning and facilitates the engineering of photoreceptors for optogenetic tools. Int J Biol Macromol 2024; 274:133407. [PMID: 38925190 DOI: 10.1016/j.ijbiomac.2024.133407] [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: 02/06/2024] [Revised: 06/14/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
Abstract
Cyanobacteriochromes (CBCRs) are distinctive tetrapyrrole (bilin)-binding photoreceptors exclusively found in cyanobacteria. Unlike canonical phytochromes, CBCRs require only a GAF (cGMP-phosphodiesterase/adenylate cyclase/FhlA) domain for autolyase activity to form a bilin adduct via a Cys residue and cis-trans photoisomerization. Apart from the canonical Cys, which attaches covalently to C31 in the A-ring of the bilin, some GAF domains of CBCRs contain a second-Cys in the Asp-Xaa-Cys-Phe (DXCF) motif, responsible for isomerization of phycocyanobilin (PCB) to phycoviolobilin (PVB) and/or for the formation of a reversible 2nd thioether linkage to the C10. Unlike green/teal-absorbing GAF proteins lacking ligation activity, the second-Cys in another teal-absorbing lineage (DXCF blue/teal group) exhibits both isomerization and ligation activity due to the presence of the Tyr instead of His next to the canonical Cys. Herein, we discovered an atypical CBCR GAF protein, Tpl7205g1, belonging to the DXCF blue/teal group, but having His instead of Tyr next to the first-Cys. Consistent with its subfamily, the second-Cys of Tpl7205g1 did not form a thioether linkage at C10 of PCB, showing only isomerization activity. Instead of forming 2nd thioether linkage, this novel GAF protein exhibits a pH-dependent photocycle between protonated 15Z and deprotonated 15E. Site-directed mutagenesis to the GAF scaffolds revealed its combined characteristics, including properties of teal-DXCF CBCRs and red/green-absorbing CBCRs (XRG CBCRs), suggesting itself as the evolutionary bridge between the two CBCR groups. Our study thus sheds light on the expanded spectral tuning characteristics of teal-light absorbing CBCRs and enhances feasibility of engineering these photoreceptors.
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Affiliation(s)
- Hee Wook Yang
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Young Won Kim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Yvette Villafani
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Ji Young Song
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea.
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26
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Vorländer MK, Rothe P, Kleifeld J, Cormack ED, Veleti L, Riabov-Bassat D, Fin L, Phillips AW, Cochella L, Plaschka C. Mechanism for the initiation of spliceosome disassembly. Nature 2024; 632:443-450. [PMID: 38925148 DOI: 10.1038/s41586-024-07741-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
Precursor-mRNA (pre-mRNA) splicing requires the assembly, remodelling and disassembly of the multi-megadalton ribonucleoprotein complex called the spliceosome1. Recent studies have shed light on spliceosome assembly and remodelling for catalysis2-6, but the mechanism of disassembly remains unclear. Here we report cryo-electron microscopy structures of nematode and human terminal intron lariat spliceosomes along with biochemical and genetic data. Our results uncover how four disassembly factors and the conserved RNA helicase DHX15 initiate spliceosome disassembly. The disassembly factors probe large inner and outer spliceosome surfaces to detect the release of ligated mRNA. Two of these factors, TFIP11 and C19L1, and three general spliceosome subunits, SYF1, SYF2 and SDE2, then dock and activate DHX15 on the catalytic U6 snRNA to initiate disassembly. U6 therefore controls both the start5 and end of pre-mRNA splicing. Taken together, our results explain the molecular basis of the initiation of canonical spliceosome disassembly and provide a framework to understand general spliceosomal RNA helicase control and the discard of aberrant spliceosomes.
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Affiliation(s)
- Matthias K Vorländer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Patricia Rothe
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Justus Kleifeld
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Eric D Cormack
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lalitha Veleti
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Daria Riabov-Bassat
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Laura Fin
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Alex W Phillips
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Clemens Plaschka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
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27
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Akbudak MA, Cirik N, Erdeger SN, Filiz E, Dogu S, Bor M. GpEF1A: a novel lysine methyltransferase gene from Gypsophila perfoliata L. involved in boron homeostasis. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:727-734. [PMID: 38781082 DOI: 10.1111/plb.13658] [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: 08/31/2023] [Accepted: 03/30/2024] [Indexed: 05/25/2024]
Abstract
Rapid accumulation of boron (B) leads to toxicity in plant tissues, and the narrow gap between deficiency and toxicity makes it difficult to adjust essential B levels in soil for plant productivity. Therefore, understanding different aspects of B tolerance is necessary to provide new and valid solutions to B toxicity. Gypsophila perfoliata stands out as a remarkable example of a B-tolerant plant, with a natural propensity to thrive in environments such as B mines and soils enriched with high levels of B. In this study, a yeast functional screening experiment was conducted using cDNA libraries from G. perfoliata leaf and root cells for B tolerance. Ten colonies from the leaf library grew in 80 mm boric acid, while none emerged from the root library. Analysis of isolated cDNAs showed identical sequences and a unique motif related to B tolerance. The gene GpEF1A was identified in the tolerant yeast colonies, with predicted structural features suggesting its role, and RT-qPCR indicating increased expression under B stress. A regulatory role for EF1A lysine methylation was proposed in mammalian cells and fungi because of its dynamic and inducible nature under environmental constraints. This could also be relevant for plant cells, as the high similarity of the GpEF1A gene in some salt-tolerant plants might indicate the upregulation of EF1A as a conserved way to cope with abiotic stress conditions. This report represents the first instance of involvement of GpEF1A in B tolerance, and further detailed studies are necessary to understand other components of this tolerance mechanism.
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Affiliation(s)
- M A Akbudak
- Department of Agricultural Biotechnology, Akdeniz University, Antalya, Türkiye
| | - N Cirik
- Department of Agricultural Biotechnology, Akdeniz University, Antalya, Türkiye
| | - S N Erdeger
- Department of Agricultural Biotechnology, Akdeniz University, Antalya, Türkiye
| | - E Filiz
- Cilimli Vocational School, Duzce University, Duzce, Türkiye
| | - S Dogu
- Meram Vocational School, Necmettin Erbakan University, Konya, Türkiye
| | - M Bor
- Department of Biology, Ege University, Izmir, Türkiye
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28
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Singh D, Tripathi P, Sharma R, Grover S, Batra JK. Role of a substrate binding pocket in the amino terminal domain of Mycobacterium tuberculosis caseinolytic protease B (ClpB) in its function. J Biomol Struct Dyn 2024; 42:6189-6199. [PMID: 37418201 DOI: 10.1080/07391102.2023.2232032] [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: 12/28/2022] [Accepted: 06/27/2023] [Indexed: 07/08/2023]
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis when infects the host encounters several stresses within the host, resulting in aggregation of its proteins. To resolve this problem Mtb uses chaperones to either repair the damage or degrade the aggregated proteins. Mtb caseinolytic protein B (ClpB) helps in the prevention of aggregation and also resolubilization of aggregated proteins in bacteria, which is important for the survival of Mtb in the host. To function optimally, ClpB associates with its co-partners DnaK, DnaJ, and GrpE. The role of N-terminal domain (NTD) of Mtb ClpB in its function is not well understood. In this context, we investigated the interaction of three substrate mimicking peptides with the NTD of Mtb ClpB in silico. A substrate binding pocket, within the NTD of ClpB comprising of residues L136, R137, E138, K142, R144, R148, V149, Y158, and Y162 forming an ɑ-helix was thus identified. The residues L136 and R137 of the ɑ-helix were found to be important for the interaction of DnaK to ClpB. Further, nine single alanine recombinant variants of the identified residues were generated. As compared to the wild-type Mtb ClpB all the Mtb ClpB variants generated in this study were found to have reduced ATPase and protein refolding activity indicating the importance of the substrate binding pocket in ClpB function. The study demonstrates that the NTD of Mtb ClpB is important for its substrate interaction activity, and the substrate binding pocket identified in this study plays a crucial role in this interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Digvijay Singh
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | | | - Rahul Sharma
- Department of Molecular Medicine, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Sonam Grover
- Department of Molecular Medicine, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Janendra K Batra
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
- ICMR-National Institute of Pathology, Safdarjung Hospital Complex, New Delhi, India
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29
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Hamm JN, Liao Y, von Kügelgen A, Dombrowski N, Landers E, Brownlee C, Johansson EMV, Whan RM, Baker MAB, Baum B, Bharat TAM, Duggin IG, Spang A, Cavicchioli R. The parasitic lifestyle of an archaeal symbiont. Nat Commun 2024; 15:6449. [PMID: 39085207 PMCID: PMC11291902 DOI: 10.1038/s41467-024-49962-y] [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: 04/26/2024] [Accepted: 06/25/2024] [Indexed: 08/02/2024] Open
Abstract
DPANN archaea are a diverse group of microorganisms characterised by small cells and reduced genomes. To date, all cultivated DPANN archaea are ectosymbionts that require direct cell contact with an archaeal host species for growth and survival. However, these interactions and their impact on the host species are poorly understood. Here, we show that a DPANN archaeon (Candidatus Nanohaloarchaeum antarcticus) engages in parasitic interactions with its host (Halorubrum lacusprofundi) that result in host cell lysis. During these interactions, the nanohaloarchaeon appears to enter, or be engulfed by, the host cell. Our results provide experimental evidence for a predatory-like lifestyle of an archaeon, suggesting that at least some DPANN archaea may have roles in controlling host populations and their ecology.
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Affiliation(s)
- Joshua N Hamm
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia.
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Hoorn, The Netherlands, 1797 SZ.
| | - Yan Liao
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Andriko von Kügelgen
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Hoorn, The Netherlands, 1797 SZ
| | - Evan Landers
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Christopher Brownlee
- Biological Resources Imaging Laboratory, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW, 2052, Australia
- Fluorescence Analysis Facility, Molecular Horizons, University of Wollongong, Keiraville, NSW, 2522, Australia
| | - Emma M V Johansson
- Biological Resources Imaging Laboratory, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Renee M Whan
- Katharina Gaus Light Microscopy Facility, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Matthew A B Baker
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Buzz Baum
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Iain G Duggin
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Hoorn, The Netherlands, 1797 SZ
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
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Kang Y, Wang J, Zhu C, Zheng M, Li Z. Unveiling the genomic diversity and ecological impact of phage communities in hospital wastewater. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135353. [PMID: 39094306 DOI: 10.1016/j.jhazmat.2024.135353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 07/13/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024]
Abstract
Phages are pivotal in shaping microbial communities and biogeochemical cycles, while our understanding of the diversity, functions potential, and resistance gene carriage of phages in hospital wastewater (HWW) remains limited. We collected influent and effluent samples from the 3 hospital wastewater treatment plants (HWTPs) to assess the diversity and fate of phages, the interactions between phages and hosts, and the presence of resistance genes and auxiliary metabolic genes (AMGs) encoded by phages. Compared to influent, effluent showed reduced phage abundance and altered composition, with decreases in Microviridae and Inoviridae. The gene-sharing network highlights that many phages in HWW are not classified in known viral genera, suggesting HWW as a rich source of new viruses. There was a significant association between phages and microorganisms, with approximately 32.57 % of phages expected to be capable of infecting microbial hosts, characterized primarily by lytic activity. A total of 8 unique antibiotic resistance genes, 13 unique metal resistance genes, and 5 mobile genetic elements were detected in 3 HWTPs phageomes. Phage AMGs have the potential to influence carbon, nitrogen, phosphorus, and sulfur metabolism, impacting biogeochemical cycles. This study reveals the genomic diversity and ecological role of phages in HWTPs, highlighting their environmental and ecosystem impact.
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Affiliation(s)
- Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102200, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Caizhong Zhu
- The Fourth Medical Center of Chinese PLA General Hospital, China
| | - Meiqin Zheng
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China.
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102200, China.
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31
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Reddy DJ, Guntuku G, Palla MS. Advancements in nanobody generation: Integrating conventional, in silico, and machine learning approaches. Biotechnol Bioeng 2024. [PMID: 39054738 DOI: 10.1002/bit.28816] [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: 05/09/2024] [Revised: 07/08/2024] [Accepted: 07/13/2024] [Indexed: 07/27/2024]
Abstract
Nanobodies, derived from camelids and sharks, offer compact, single-variable heavy-chain antibodies with diverse biomedical potential. This review explores their generation methods, including display techniques on phages, yeast, or bacteria, and computational methodologies. Integrating experimental and computational approaches enhances understanding of nanobody structure and function. Future trends involve leveraging next-generation sequencing, machine learning, and artificial intelligence for efficient candidate selection and predictive modeling. The convergence of traditional and computational methods promises revolutionary advancements in precision biomedical applications such as targeted drug delivery and diagnostics. Embracing these technologies accelerates nanobody development, driving transformative breakthroughs in biomedicine and paving the way for precision medicine and biomedical innovation.
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Affiliation(s)
- D Jagadeeswara Reddy
- Pharmaceutical Biotechnology Division, A.U. College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, India
| | - Girijasankar Guntuku
- Pharmaceutical Biotechnology Division, A.U. College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, India
| | - Mary Sulakshana Palla
- GITAM School of Pharmacy, GITAM Deemed to be University, Rushikonda, Visakhapatnam, India
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32
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Hying ZT, Miller TJ, Loh CY, Bazurto JV. Glycine betaine metabolism is enabled in Methylorubrum extorquens PA1 by alterations to dimethylglycine dehydrogenase. Appl Environ Microbiol 2024; 90:e0209023. [PMID: 38534142 PMCID: PMC11267896 DOI: 10.1128/aem.02090-23] [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: 11/17/2023] [Accepted: 02/22/2024] [Indexed: 03/28/2024] Open
Abstract
Low nutrient availability is a key characteristic of the phyllosphere (the aerial surface of plants). Phyllospheric bacteria utilize a wide array of carbon sources generated by plant hosts. Glycine betaine (GB) is a plant-derived compound that can be metabolized by certain members of the phyllosphere microbiota. Metabolism of glycine betaine generates formaldehyde, an intermediate of methylotrophic metabolism, leading us to investigate how the ubiquitous plant colonizing bacterium Methylorubrum extorquens PA1 might metabolize GB encountered in its native environment. M. extorquens PA1 cannot utilize GB as a sole carbon source. Through suppressor mutation analysis, we show that M. extorquens PA1 encodes a conserved GB utilization pathway that can be activated by single point mutations conferring GB utilization as a carbon source. We identified the gene cluster encoding the GB catabolic enzymes and found that gene expression was induced in the presence of GB. We show that utilization of GB is conserved among representative Methylobacterium species and generates the one-carbon metabolism intermediate formaldehyde, which M. extorquens utilizes as a source of energy. Our results support a model where suppressor mutations in Mext_3745 or ftsH (Mext_4840) prevent the degradation of the dimethylglycine dehydrogenase subunit DgcB by the membrane integral protease FtsH, conferring the ability to utilize GB by either (i) restoring stable membrane topology of DgcB or (ii) decreasing FtsH protease activity, respectively. Both mutations alleviate the bottleneck at the second step of GB degradation catalyzed by DgcAB.IMPORTANCEOvercoming low nutrient availability is a challenge many bacteria encounter in the environment. Facultative methylotrophs are able to utilize one-carbon and multi-carbon compounds as carbon and energy sources. The utilization of plant-derived glycine betaine (GB) represents a possible source of multi-carbon and one-carbon substrates. The metabolism of glycine betaine produces formaldehyde and glycine, which may be used simultaneously by facultative methylotrophs. However, the genes required for the utilization of GB in the ubiquitous plant-associated bacterium Methylorubrum extorquens have yet to be identified or described. Our work identifies and validates the genes required for glycine betaine metabolism in M. extorquens and shows that it directly intersects with methylotrophic metabolism through the production of formaldehyde.
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Affiliation(s)
- Zachary T. Hying
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Tyler J. Miller
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Chin Yi Loh
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Jannell V. Bazurto
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
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Premachandre CK, Vaz PK, Sharma S, Kanci Condello A, Browning GF, Wawegama NK. Genes required for survival and proliferation of Mycoplasma bovis in association with host cells. Appl Environ Microbiol 2024; 90:e0068724. [PMID: 38864628 PMCID: PMC11267936 DOI: 10.1128/aem.00687-24] [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: 04/29/2024] [Accepted: 05/19/2024] [Indexed: 06/13/2024] Open
Abstract
Mycoplasma bovis is an important emerging pathogen of cattle and bison, but our understanding of the genetic basis of its interactions with its host is limited. The aim of this study was to identify genes of M. bovis required for interaction and survival in association with host cells. One hundred transposon-induced mutants of the type strain PG45 were assessed for their capacity to survive and proliferate in Madin-Darby bovine kidney cell cultures. The growth of 19 mutants was completely abrogated, and 47 mutants had a prolonged doubling time compared to the parent strain. All these mutants had a similar growth pattern to the parent strain PG45 in the axenic media. Thirteen genes previously classified as dispensable for the axenic growth of M. bovis were found to be essential for the growth of M. bovis in association with host cells. In most of the mutants with a growth-deficient phenotype, the transposon was inserted into a gene involved in transportation or metabolism. This included genes coding for ABC transporters, proteins related to carbohydrate, nucleotide and protein metabolism, and membrane proteins essential for attachment. It is likely that these genes are essential not only in vitro but also for the survival of M. bovis in infected animals. IMPORTANCE Mycoplasma bovis causes chronic bronchopneumonia, mastitis, arthritis, keratoconjunctivitis, and reproductive tract disease in cattle around the globe and is an emerging pathogen in bison. Control of mycoplasma infections is difficult in the absence of appropriate antimicrobial treatment or effective vaccines. A comprehensive understanding of host-pathogen interactions and virulence factors is important to implement more effective control methods against M. bovis. Recent studies of other mycoplasmas with in vitro cell culture models have identified essential virulence genes of mycoplasmas. Our study has identified genes of M. bovis required for survival in association with host cells, which will pave the way to a better understanding of host-pathogen interactions and the role of specific genes in the pathogenesis of disease caused by M. bovis.
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Affiliation(s)
- Chintha K. Premachandre
- Asia-Pacific Center for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Paola K. Vaz
- Asia-Pacific Center for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Shukriti Sharma
- Asia-Pacific Center for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Anna Kanci Condello
- Asia-Pacific Center for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Glenn F. Browning
- Asia-Pacific Center for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Nadeeka K. Wawegama
- Asia-Pacific Center for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
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Gambino M, Kushwaha SK, Wu Y, van Haastrecht P, Klein-Sousa V, Lutz VT, Bejaoui S, Jensen CMC, Bojer MS, Song W, Xiao M, Taylor NMI, Nobrega FL, Brøndsted L. Diversity and phage sensitivity to phages of porcine enterotoxigenic Escherichia coli. Appl Environ Microbiol 2024; 90:e0080724. [PMID: 38940562 PMCID: PMC11267873 DOI: 10.1128/aem.00807-24] [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: 05/15/2024] [Accepted: 06/05/2024] [Indexed: 06/29/2024] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) is a diverse and poorly characterized E. coli pathotype that causes diarrhea in humans and animals. Phages have been proposed for the veterinary biocontrol of ETEC, but effective solutions require understanding of porcine ETEC diversity that affects phage infection. Here, we sequenced and analyzed the genomes of the PHAGEBio ETEC collection, gathering 79 diverse ETEC strains isolated from European pigs with post-weaning diarrhea (PWD). We identified the virulence factors characterizing the pathotype and several antibiotic resistance genes on plasmids, while phage resistance genes and other virulence factors were mostly chromosome encoded. We experienced that ETEC strains were highly resistant to Enterobacteriaceae phage infection. It was only by enrichment of numerous diverse samples with different media and conditions, using the 41 ETEC strains of our collection as hosts, that we could isolate two lytic phages that could infect a large part of our diverse ETEC collection: vB_EcoP_ETEP21B and vB_EcoS_ETEP102. Based on genome and host range analyses, we discussed the infection strategies of the two phages and identified components of lipopolysaccharides ( LPS) as receptors for the two phages. Our detailed computational structural analysis highlights several loops and pockets in the tail fibers that may allow recognition and binding of ETEC strains, also in the presence of O-antigens. Despite the importance of receptor recognition, the diversity of the ETEC strains remains a significant challenge for isolating ETEC phages and developing sustainable phage-based products to address ETEC-induced PWD.IMPORTANCEEnterotoxigenic Escherichia coli (ETEC)-induced post-weaning diarrhea is a severe disease in piglets that leads to weight loss and potentially death, with high economic and animal welfare costs worldwide. Phage-based approaches have been proposed, but available data are insufficient to ensure efficacy. Genome analysis of an extensive collection of ETEC strains revealed that phage defense mechanisms were mostly chromosome encoded, suggesting a lower chance of spread and selection by phage exposure. The difficulty in isolating lytic phages and the molecular and structural analyses of two ETEC phages point toward a multifactorial resistance of ETEC to phage infection and the importance of extensive phage screenings specifically against clinically relevant strains. The PHAGEBio ETEC collection and these two phages are valuable tools for the scientific community to expand our knowledge on the most studied, but still enigmatic, bacterial species-E. coli.
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Affiliation(s)
- Michela Gambino
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
- Institute of Conservation, The Royal Danish Academy, Copenhagen, Denmark
| | - Simran Krishnakant Kushwaha
- School of Biological Sciences, Faculty of Environmental & Life Sciences, University of Southampton, Southampton, United Kingdom
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Yi Wu
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Pauline van Haastrecht
- School of Biological Sciences, Faculty of Environmental & Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Victor Klein-Sousa
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Veronika T. Lutz
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Semeh Bejaoui
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Martin S. Bojer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Nicholas M. I. Taylor
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Franklin L. Nobrega
- School of Biological Sciences, Faculty of Environmental & Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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Shi Z, Long X, Zhang C, Chen Z, Usman M, Zhang Y, Zhang S, Luo G. Viral and Bacterial Community Dynamics in Food Waste and Digestate from Full-Scale Biogas Plants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:13010-13022. [PMID: 38989650 DOI: 10.1021/acs.est.4c04109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Anaerobic digestion (AD) is commonly used in food waste treatment. Prokaryotic microbial communities in AD of food waste have been comprehensively studied. The role of viruses, known to affect microbial dynamics and metabolism, remains largely unexplored. This study employed metagenomic analysis and recovered 967 high-quality viral bins within food waste and digestate derived from 8 full-scale biogas plants. The diversity of viral communities was higher in digestate. In silico predictions linked 20.8% of viruses to microbial host populations, highlighting possible virus predators of key functional microbes. Lineage-specific virus-host ratio varied, indicating that viral infection dynamics might differentially affect microbial responses to the varying process parameters. Evidence for virus-mediated gene transfer was identified, emphasizing the potential role of viruses in controlling the microbiome. AD altered the specific process parameters, potentially promoting a shift in viral lifestyle from lysogenic to lytic. Viruses encoding auxiliary metabolic genes (AMGs) were involved in microbial carbon and nutrient cycling, and most AMGs were transcriptionally expressed in digestate, meaning that viruses with active functional states were likely actively involved in AD. These findings provided a comprehensive profile of viral and bacterial communities and expanded knowledge of the interactions between viruses and hosts in food waste and digestate.
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Affiliation(s)
- Zhijian Shi
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Xinyi Long
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Chao Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Zheng Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Muhammad Usman
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Yalei Zhang
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Shicheng Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
- Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
- Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, China
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36
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Crandall JG, Zhou X, Rokas A, Hittinger CT. Specialization restricts the evolutionary paths available to yeast sugar transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.22.604696. [PMID: 39091816 PMCID: PMC11291069 DOI: 10.1101/2024.07.22.604696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Functional innovation at the protein level is a key source of evolutionary novelties. The constraints on functional innovations are likely to be highly specific in different proteins, which are shaped by their unique histories and the extent of global epistasis that arises from their structures and biochemistries. These contextual nuances in the sequence-function relationship have implications both for a basic understanding of the evolutionary process and for engineering proteins with desirable properties. Here, we have investigated the molecular basis of novel function in a model member of an ancient, conserved, and biotechnologically relevant protein family. These Major Facilitator Superfamily sugar porters are a functionally diverse group of proteins that are thought to be highly plastic and evolvable. By dissecting a recent evolutionary innovation in an α-glucoside transporter from the yeast Saccharomyces eubayanus, we show that the ability to transport a novel substrate requires high-order interactions between many protein regions and numerous specific residues proximal to the transport channel. To reconcile the functional diversity of this family with the constrained evolution of this model protein, we generated new, state-of-the-art genome annotations for 332 Saccharomycotina yeast species spanning approximately 400 million years of evolution. By integrating phylogenetic and phenotypic analyses across these species, we show that the model yeast α-glucoside transporters likely evolved from a multifunctional ancestor and became subfunctionalized. The accumulation of additive and epistatic substitutions likely entrenched this subfunction, which made the simultaneous acquisition of multiple interacting substitutions the only reasonably accessible path to novelty.
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Affiliation(s)
- Johnathan G. Crandall
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
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Sharma N, Gupta M, Anand P, Akhter Y, Al-Dayan N, Majed HA, Biswas S, Ali S, Sarwat M. Mechanistic Insight into the Autophagic and Apoptotic Activity of Kaempferol on Liver Cancer Cells. Onco Targets Ther 2024; 17:579-601. [PMID: 39071955 PMCID: PMC11283267 DOI: 10.2147/ott.s460359] [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: 01/18/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024] Open
Abstract
Background The accumulation of poorly folded protein in the endoplasmic reticulum (ER) promotes ER stress and contributes to the pathogenesis of hepatocellular carcinoma (HCC). Current therapies have various adverse effects, therefore, laying the need for an alternative approach. Kaempferol (KP), a naturally occurring flavonoid, possesses potent anti-proliferative properties against various cancer cells. Nevertheless, its involvement in HCC remains relatively unexplored, particularly regarding its influence on apoptosis and autophagy pathways. Methods The effect of KP on cell viability, and motility of Hep3B cells was evaluated by MTT, and scratch assay, respectively. Hoechst staining and FACS analysis were done to check the effect of KP on apoptosis and cell cycle progression. qRTPCR was used to evaluate the expression of several apoptosis and autophagy-related genes. KP was docked with several ER stress-related proteins involved in HCC to gain further insights into molecular mechanisms. The results of docking studies were validated with MD simulation and in vitro studies. Results Treatment with KP at different time intervals showed dose- and time-dependent growth inhibition of liver cancer cells. KP decreased motility and arrested the cell cycle at the G0/G1 phase in Hep3B cells. Additionally, in the context of HCC, the relationship between KP, apoptosis, and autophagy is significant. It induced apoptosis and autophagy in Hep3B cells by downregulating the expression of Bcl-2 and upregulated Bax and Bid, Caspase-3, Beclin-1, and LC3. KP showed a better binding affinity with Nrf2, PERK, and IRE1α among all selected proteins. Further, it reversed the protective effect of 4-PBA (ER Stress inhibitor) by inducing apoptosis and autophagy in Hep3B cells. Conclusion The study suggested KP as a potential chemopreventive agent for managing HCC by effectively inducing apoptosis and autophagy in Hep3B cells.
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Affiliation(s)
- Nidhi Sharma
- Amity Institute of Pharmacy, Amity University, Noida, Uttar Pradesh, 201301, India
| | - Meenakshi Gupta
- Amity Institute of Pharmacy, Amity University, Noida, Uttar Pradesh, 201301, India
| | - Pragya Anand
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Noura Al-Dayan
- Department of Medical Laboratory, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Hind Abdul Majed
- Department of Clinical Microbiology and Immunology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Subhrajit Biswas
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, Uttar Pradesh, 201301, India
| | - Sher Ali
- VC Office, Era University, Lucknow, Uttar Pradesh, 226003, India
| | - Maryam Sarwat
- Amity Institute of Pharmacy, Amity University, Noida, Uttar Pradesh, 201301, India
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38
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Balagopalan L, Moreno T, Qin H, Angeles BC, Kondo T, Yi J, McIntire KM, Alvinez N, Pallikkuth S, Lee ME, Yamane H, Tran AD, Youkharibache P, Cachau RE, Taylor N, Samelson LE. Generation of antitumor chimeric antigen receptors incorporating T cell signaling motifs. Sci Signal 2024; 17:eadp8569. [PMID: 39042728 DOI: 10.1126/scisignal.adp8569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/17/2024] [Indexed: 07/25/2024]
Abstract
Chimeric antigen receptor (CAR) T cells have been used to successfully treat various blood cancers, but adverse effects have limited their potential. Here, we developed chimeric adaptor proteins (CAPs) and CAR tyrosine kinases (CAR-TKs) in which the intracellular ζ T cell receptor (TCRζ) chain was replaced with intracellular protein domains to stimulate signaling downstream of the TCRζ chain. CAPs contain adaptor domains and the kinase domain of ZAP70, whereas CAR-TKs contain only ZAP70 domains. We hypothesized that CAPs and CAR-TKs would be more potent than CARs because they would bypass both the steps that define the signaling threshold of TCRζ and the inhibitory regulation of upstream molecules. CAPs were too potent and exhibited high tonic signaling in vitro. In contrast, CAR-TKs exhibited high antitumor efficacy and significantly enhanced long-term tumor clearance in leukemia-bearing NSG mice as compared with the conventional CD19-28ζ-CAR-T cells. CAR-TKs were activated in a manner independent of the kinase Lck and displayed slower phosphorylation kinetics and prolonged signaling compared with the 28ζ-CAR. Lck inhibition attenuated CAR-TK cell exhaustion and improved long-term function. The distinct signaling properties of CAR-TKs may therefore be harnessed to improve the in vivo efficacy of T cells engineered to express an antitumor chimeric receptor.
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MESH Headings
- Animals
- Receptors, Chimeric Antigen/immunology
- Receptors, Chimeric Antigen/metabolism
- Receptors, Chimeric Antigen/genetics
- Humans
- Signal Transduction/immunology
- Mice
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/genetics
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- ZAP-70 Protein-Tyrosine Kinase/metabolism
- ZAP-70 Protein-Tyrosine Kinase/genetics
- ZAP-70 Protein-Tyrosine Kinase/immunology
- Immunotherapy, Adoptive/methods
- Mice, Inbred NOD
- Cell Line, Tumor
- Phosphorylation
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Affiliation(s)
- Lakshmi Balagopalan
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Taylor Moreno
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Haiying Qin
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Benjamin C Angeles
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Taisuke Kondo
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Yi
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Katherine M McIntire
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Neriah Alvinez
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Sandeep Pallikkuth
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Mariah E Lee
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Hidehiro Yamane
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Andy D Tran
- Laboratory of Cancer Biology and Genetics (CCR Microscopy Core), National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Philippe Youkharibache
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raul E Cachau
- Integrated Data Science Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Naomi Taylor
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lawrence E Samelson
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
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Maestri A, Pons BJ, Pursey E, Chong CE, Gandon S, Custodio R, Olina A, Agapov A, Chisnall MAW, Grasso A, Paterson S, Szczelkun MD, Baker KS, van Houte S, Chevallereau A, Westra ER. The bacterial defense system MADS interacts with CRISPR-Cas to limit phage infection and escape. Cell Host Microbe 2024:S1931-3128(24)00264-6. [PMID: 39094583 DOI: 10.1016/j.chom.2024.07.005] [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: 08/09/2023] [Revised: 04/23/2024] [Accepted: 07/08/2024] [Indexed: 08/04/2024]
Abstract
The constant arms race between bacteria and their parasites has resulted in a large diversity of bacterial defenses, with many bacteria carrying multiple systems. Here, we report the discovery of a phylogenetically widespread defense system, coined methylation-associated defense system (MADS), which is distributed across gram-positive and gram-negative bacteria. MADS interacts with a CRISPR-Cas system in its native host to provide robust and durable resistance against phages. While phages can acquire epigenetic-mediated resistance against MADS, co-existence of MADS and a CRISPR-Cas system limits escape emergence. MADS comprises eight genes with predicted nuclease, ATPase, kinase, and methyltransferase domains, most of which are essential for either self/non-self discrimination, DNA restriction, or both. The complex genetic architecture of MADS and MADS-like systems, relative to other prokaryotic defenses, points toward highly elaborate mechanisms of sensing infections, defense activation, and/or interference.
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Affiliation(s)
- Alice Maestri
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Benoit J Pons
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Elizabeth Pursey
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Charlotte E Chong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK; Department of Genetics, University of Cambridge, Downing Place, Cambridge CB2 3EH, UK
| | - Sylvain Gandon
- CEFE, CNRS, Université de Montpellier, EPHE, IRD, Montpellier 34293, France
| | - Rafael Custodio
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Anna Olina
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Aleksei Agapov
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Matthew A W Chisnall
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Anita Grasso
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Kate S Baker
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK; Department of Genetics, University of Cambridge, Downing Place, Cambridge CB2 3EH, UK
| | - Stineke van Houte
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Anne Chevallereau
- Université Paris Cité, CNRS, INSERM, Institut Cochin, Paris 75014, France.
| | - Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK.
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40
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Petrone ME, Grove J, Mélade J, Mifsud JCO, Parry RH, Marzinelli EM, Holmes EC. A ~40-kb flavi-like virus does not encode a known error-correcting mechanism. Proc Natl Acad Sci U S A 2024; 121:e2403805121. [PMID: 39018195 PMCID: PMC11287256 DOI: 10.1073/pnas.2403805121] [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: 02/22/2024] [Accepted: 06/13/2024] [Indexed: 07/19/2024] Open
Abstract
It is commonly held that there is a fundamental relationship between genome size and error rate, manifest as a notional "error threshold" that sets an upper limit on genome sizes. The genome sizes of RNA viruses, which have intrinsically high mutation rates due to a lack of mechanisms for error correction, must therefore be small to avoid accumulating an excessive number of deleterious mutations that will ultimately lead to population extinction. The proposed exceptions to this evolutionary rule are RNA viruses from the order Nidovirales (such as coronaviruses) that encode error-correcting exonucleases, enabling them to reach genome lengths greater than 40 kb. The recent discovery of large-genome flavi-like viruses (Flaviviridae), which comprise genomes up to 27 kb in length yet seemingly do not encode exonuclease domains, has led to the proposal that a proofreading mechanism is required to facilitate the expansion of nonsegmented RNA virus genomes above 30 kb. Herein, we describe a ~40 kb flavi-like virus identified in a Haliclona sponge metatranscriptome that does not encode a known exonuclease. Structural analysis revealed that this virus may have instead captured cellular domains associated with nucleic acid metabolism that have not been previously found in RNA viruses. Phylogenetic inference placed this virus as a divergent pesti-like lineage, such that we have provisionally termed it "Maximus pesti-like virus." This virus represents an instance of a flavi-like virus achieving a genome size comparable to that of the Nidovirales and demonstrates that RNA viruses have evolved multiple solutions to overcome the error threshold.
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Affiliation(s)
- Mary E. Petrone
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong Special Administrative Region, China
| | - Joe Grove
- MRC-University of Glasgow Centre for Virus Research, GlasgowG61 1QH, United Kingdom
| | - Julien Mélade
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
| | - Jonathon C. O. Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
| | - Rhys H. Parry
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD4067, Australia
| | - Ezequiel M. Marzinelli
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong Special Administrative Region, China
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41
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Jin J, Jia Z. Characterization of Potential Plastic-Degradation Enzymes from Marine Bacteria. ACS OMEGA 2024; 9:32185-32192. [PMID: 39072070 PMCID: PMC11270687 DOI: 10.1021/acsomega.4c04843] [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: 05/22/2024] [Revised: 06/29/2024] [Accepted: 07/05/2024] [Indexed: 07/30/2024]
Abstract
Polyethylene terephthalate (PET) and polyethylene (PE) are prominent polymer materials that comprise a significant portion of commercial plastic waste. Their durability and slow degradation rate have resulted in significant accumulation of plastic on Earth. In a recent study, macrotranscriptomic profiling of a reconstituted marine bacterial community identified 10 putative enzymes capable of directly acting on PE or PET (PEases or PETases). Among these enzymes, three recombinant proteins were reported to possess PE degradation activity. To select potential plastic degrading enzyme candidates for protein engineering efforts, we expressed and purified eight out of the 10 candidates, excluding two due to poor expression and/or solubility. Notably, several candidate proteins displayed significant esterase activity on p-nitrophenyl butyrate and exhibited unexpected thermostability despite their marine origin. Additionally, we observed dose- and time-dependent hydrolytic activity on the PET trimer substrate. Structural analysis and mutagenesis of a candidate protein confirmed the presence of catalytic triad residues, classifying it as an esterase. Furthermore, we elucidated the structural importance of the two disulfide bonds. Through point mutation experiments, we observed an enhanced hydrolytic activity of a selected enzyme candidate on PET nanoparticles. Our findings challenge the classification of the enzymes directly acting on PE and highlight the significance and complexity of validating PE degradation enzymes identified through metagenomic analysis.
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Affiliation(s)
- Jin Jin
- Department of Biomedical
and Molecular Sciences, Queen’s University, 18 Stuart Street, Kingston, ON KL7
3N6, Canada
| | - Zongchao Jia
- Department of Biomedical
and Molecular Sciences, Queen’s University, 18 Stuart Street, Kingston, ON KL7
3N6, Canada
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42
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Das A, Franco JA, Mulcahy B, Wang L, Chapman D, Jaisinghani C, Pruitt BL, Zhen M, Goodman MB. C. elegans touch receptor neurons direct mechanosensory complex organization via repurposing conserved basal lamina proteins. Curr Biol 2024; 34:3133-3151.e10. [PMID: 38964319 PMCID: PMC11283674 DOI: 10.1016/j.cub.2024.06.013] [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: 12/05/2023] [Revised: 05/13/2024] [Accepted: 06/06/2024] [Indexed: 07/06/2024]
Abstract
The sense of touch is conferred by the conjoint function of somatosensory neurons and skin cells. These cells meet across a gap filled by a basal lamina, an ancient structure found in metazoans. Using Caenorhabditis elegans, we investigate the composition and ultrastructure of the extracellular matrix at the epidermis and touch receptor neuron (TRN) interface. We show that membrane-matrix complexes containing laminin, nidogen, and the MEC-4 mechano-electrical transduction channel reside at this interface and are central to proper touch sensation. Interestingly, the dimensions and spacing of these complexes correspond with the discontinuous beam-like extracellular matrix structures observed in serial-section transmission electron micrographs. These complexes fail to coalesce in touch-insensitive extracellular matrix mutants and in dissociated neurons. Loss of nidogen reduces the density of mechanoreceptor complexes and the amplitude of the touch-evoked currents they carry. Thus, neuron-epithelium cell interfaces are instrumental in mechanosensory complex assembly and function. Unlike the basal lamina ensheathing the pharynx and body wall muscle, nidogen recruitment to the puncta along TRNs is not dependent upon laminin binding. MEC-4, but not laminin or nidogen, is destabilized by point mutations in the C-terminal Kunitz domain of the extracellular matrix component, MEC-1. These findings imply that somatosensory neurons secrete proteins that actively repurpose the basal lamina to generate special-purpose mechanosensory complexes responsible for vibrotactile sensing.
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Affiliation(s)
- Alakananda Das
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Joy A Franco
- Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Ben Mulcahy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Lingxin Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Dail Chapman
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Chandni Jaisinghani
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Beth L Pruitt
- Departments of Mechanical Engineering and Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Mei Zhen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Miriam B Goodman
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA.
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Li Y, Xu T, Tu Y, Li T, Wei Y, Zhou Y. An aldolase-dependent phloroglucinol degradation pathway in Collinsella sp. zg1085. Appl Environ Microbiol 2024:e0104724. [PMID: 39028195 DOI: 10.1128/aem.01047-24] [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: 05/28/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024] Open
Abstract
Phloroglucinol (1,3,5-trihydroxybenzene) is a key intermediate in the degradation of polyphenols such as flavonoids and hydrolysable tannins and can be used by certain bacteria as a carbon and energy source for growth. The identification of enzymes that participate in the fermentation of phloroglucinol to acetate and butyrate in Clostridia was recently reported. In this study, we present the discovery and characterization of a novel metabolic pathway for phloroglucinol degradation in the bacterium Collinsella sp. zg1085, from marmot respiratory tract. In both the Clostridial and Collinsella pathways, phloroglucinol is first reduced to dihydrophoroglucinol by the NADPH-dependent phloroglucinol reductase (PGR), followed by ring opening to form (S)-3-hydroxy-5-oxohexanoate by a Mn2+-dependent dihydrophloroglucinol cyclohydrolase (DPGC). In the Collinsella pathway, (S)-3-hydroxy-5-oxohexanoate is then cleaved to form malonate semialdehyde and acetone by a newly identified aldolase (HOHA). Finally, a NADP+-dependent malonate-semialdehyde dehydrogenase converts malonate semialdehyde to CO2 and acetyl-CoA, an intermediate in carbon and energy metabolism. Recombinant expression of the Collinsella PGR, DPGC, and HOHA in E. coli enabled the conversion of phloroglucinol into acetone, providing support for the proposed pathway. Experiments with Olsenella profusa, another bacterium containing the gene cluster of interest, show that the PGR, DPGC, HOHA, and MSDH are induced by phloroglucinol. Our findings add to the variety of metabolic pathways for the degradation of phloroglucinol, a widely distributed phenolic compound, in the anaerobic microbiome.IMPORTANCEPhloroglucinol is an important intermediate in the bacterial degradation of polyphenols, a highly abundant class of plant natural products. Recent research has identified key enzymes of the phloroglucinol degradation pathway in butyrate-producing anaerobic bacteria, which involves cleavage of a linear triketide intermediate by a beta ketoacid cleavage enzyme, requiring acetyl-CoA as a co-substrate. This paper reports a variant of the pathway in the lactic acid bacterium Collinsella sp. zg1085, which involves cleavage of the triketide intermediate by a homolog of deoxyribose-5-phosphate aldolase, highlighting the variety of mechanisms for phloroglucinol degradation by different anaerobic bacterial taxa.
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Affiliation(s)
- Yating Li
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Tong Xu
- Department of Pharmacy, Northern Jiangsu People's Hospital, Clinical Medical School of Yangzhou University, Yangzhou, Jiangsu, China
| | - Yanqin Tu
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Tong Li
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yan Zhou
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
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Burke BE, Rocha SM, Campbell C, Creissen E, Tjalkens RB, Ma W, Henao-Tamayo M, Schountz T. Discrimination of Jamaican fruit bat lymphocytes by flow cytometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.604131. [PMID: 39071331 PMCID: PMC11275888 DOI: 10.1101/2024.07.18.604131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Bats are natural reservoir hosts of many important zoonotic viruses but because there are few immunological reagents and breeding colonies available for infectious disease research, little is known about their immune responses to infection. We established a breeding colony Jamaican fruit bats ( Artibeus jamaicensis ) to study bat virology and immunology. The species is used as a natural reservoir model for H18N11 influenza A virus, and as a surrogate model for SARS-CoV-2, MERS-CoV and Tacaribe virus. As part of our ongoing efforts to develop this model organism, we sought to identify commercially available monoclonal antibodies (mAb) for profiling Jamaican fruit bat lymphocytes. We identified several cross-reactive mAb that can be used to identify T and B cells; however, we were unable to identify mAb for three informative T cell markers, CD3γ, CD4 and CD8α. We targeted these markers for the generation of hybridomas, and identified several clones to each that can be used with flow cytometry and fluorescence microscopy. Specificity of the monoclonal antibodies was validated by sorting lymphocytes, followed by PCR identification of confirmatory transcripts. Spleens of Jamaican fruit bats possess about half the number of T cells than do human or mouse spleens, and we identified an unusual population of cells that expressed the B cell marker CD19 and the T cell marker CD3. The availability of these monoclonal antibodies will permit a more thorough examination of adaptive immune responses in Jamaican fruit bats that should help clarify how the bats control viral infections and without disease. Importance Bats naturally host a number of viruses without disease, but which can cause significant disease in humans. Virtually nothing is known about adaptive immune responses in bats because of a lack of immunological tools to examine such responses. We have begun to address this deficiency by identifying several commercially available monoclonal antibodies to human and mouse antigens that are cross-reactive to Jamaican fruit bat lymphocyte orthologs. We also generated monoclonal antibodies to Jamaican fruit bat CD3γ, CD4 and CD8α that are suitable for identifying T cell subsets by flow cytometry and immunofluorescent staining of fixed tissues. Together, these reagents will allow a more detailed examination of lymphocyte populations in Jamaican fruit bats.
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45
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de Dios-Blázquez L, Cano-Argüelles AL, Pérez-Sánchez R, González-Sánchez M, Oleaga A. First data on cholesterol metabolism in Ornithodoros argasid ticks: Molecular and functional characterization of the N-terminal domain of Niemann-Pick C1 proteins. Ticks Tick Borne Dis 2024; 15:102382. [PMID: 39032307 DOI: 10.1016/j.ttbdis.2024.102382] [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: 04/29/2024] [Revised: 06/21/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
Cholesterol is a molecule vital for tick physiology, but ticks cannot synthesize it and rely on dietary cholesterol. Therefore, tick proteins involved in cholesterol absorption and transport, such as the Niemann-Pick type C1 domain-containing (NPC1) proteins, are promising targets for anti-tick vaccine development. The aim of this study was to assess the structure, function, and protective efficacy of the NPC1 orthologues identified previously in the midgut transcriptomes of argasid ticks Ornithodoros erraticus and Ornithodoros moubata. For this purpose, their corresponding cDNA coding sequences were cloned and sequenced, their secondary and 3D structures were predicted, and their function was evaluated through RNAi-mediated gene knockdown and in vitro feeding on blood supplemented with ezetimibe, which inhibits cholesterol binding by NPC1 proteins. Subsequently, the protective efficacy of a recombinant form of NPC1 from O. moubata (rOmNPC1) was tested in a rabbit vaccine trial. While inhibiting cholesterol absorption with ezetimibe resulted in up to 77 % mortality in adult O. moubata, NPC1 gene knockdown and vaccination with rOmNPC1 decreased female reproductive performance in terms of the number and fertility of laid eggs. This study presents the initial molecular and functional insights into NPC1 proteins in soft ticks and supports the hypothesis that disrupting cholesterol metabolism diminishes tick viability and reproduction, rendering Niemann-Pick type C1 domain-containing proteins promising targets for drugs or vaccines.
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Affiliation(s)
- Lucía de Dios-Blázquez
- Fundación para la Investigación Biomédica del Hospital Universitario la Paz -FIBHULP-, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - Ana Laura Cano-Argüelles
- Parasitology, Institute of Natural Resources and Agrobiology of Salamanca (IRNASA, CSIC), Cordel de Merinas, 40-52, 37008, Salamanca, Spain
| | - Ricardo Pérez-Sánchez
- Parasitology, Institute of Natural Resources and Agrobiology of Salamanca (IRNASA, CSIC), Cordel de Merinas, 40-52, 37008, Salamanca, Spain
| | - María González-Sánchez
- Parasitology, Institute of Natural Resources and Agrobiology of Salamanca (IRNASA, CSIC), Cordel de Merinas, 40-52, 37008, Salamanca, Spain
| | - Ana Oleaga
- Fundación para la Investigación Biomédica del Hospital Universitario la Paz -FIBHULP-, Paseo de la Castellana, 261, 28046, Madrid, Spain.
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46
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Mazzantini D, Gherardini G, Rossi V, Celandroni F, Calvigioni M, Panattoni A, Massimino M, Lupetti A, Ghelardi E. Dissecting the role of the MS-ring protein FliF in Bacillus cereus flagella-related functions. Mol Microbiol 2024. [PMID: 39030901 DOI: 10.1111/mmi.15299] [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: 12/13/2023] [Revised: 07/05/2024] [Accepted: 07/06/2024] [Indexed: 07/22/2024]
Abstract
The flagellar MS-ring, uniquely constituted by FliF, is essential for flagellar biogenesis and functionality in several bacteria. The aim of this study was to dissect the role of FliF in the Gram-positive and peritrichously flagellated Bacillus cereus. We demonstrate that fliF forms an operon with the upstream gene fliE. In silico analysis of B. cereus ATCC 14579 FliF identifies functional domains and amino acid residues that are essential for protein functioning. The analysis of a ΔfliF mutant of B. cereus, constructed in this study using an in frame markerless gene replacement method, reveals that the mutant is unexpectedly able to assemble flagella, although in reduced amounts compared to the parental strain. Nevertheless, motility is completely abolished by fliF deletion. FliF deprivation causes the production of submerged biofilms and affects the ability of B. cereus to adhere to gastrointestinal mucins. We additionally show that the fliF deletion does not compromise the secretion of the three components of hemolysin BL, a toxin secreted through the flagellar type III secretion system. Overall, our findings highlight the important role of B. cereus FliF in flagella-related functions, being the protein required for complete flagellation, motility, mucin adhesion, and pellicle biofilms.
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Affiliation(s)
- Diletta Mazzantini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Guendalina Gherardini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Virginia Rossi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Francesco Celandroni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Marco Calvigioni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Adelaide Panattoni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Mariacristina Massimino
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Antonella Lupetti
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Emilia Ghelardi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
- Research Center Nutraceuticals and Food for Health-Nutrafood, University of Pisa, Pisa, Italy
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Wani AK, Chopra C, Ansari MA, Dar MA, Américo-Pinheiro JHP, Singh R. Characterization of thermostable carboxypeptidase from high-altitude hot spring metagenome. Int J Biol Macromol 2024; 276:133974. [PMID: 39029824 DOI: 10.1016/j.ijbiomac.2024.133974] [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: 05/29/2024] [Revised: 07/01/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
Abstract
This study explored the metagenome of the Pir Panjal Hot Spring (PPHS) to identify thermostable hydrolases. The carboxypeptidase (CarP) gene was successfully amplified and cloned into Escherichia coli DH5-α cells, followed by expression in E. coli BL21-DE3 cells. The CarP enzyme was comprehensively characterized in vitro. Sequencing analysis revealed an open reading frame encoding a functional protein of 504 amino acids, with a molecular weight of 58.65 kDa and an isoelectric point of 4.81. The CarP protein was purified using Ni-His affinity chromatography, and the experimental molecular weight matched in silico predictions. The enzyme exhibited significant thermostability and alkaliphilic properties, with optimal activity at 70 °C and pH 10.0. Additionally, the presence of Zn+2 ions at concentrations of 5 and 10 mmol/L enhanced protease activity by 1.4 and 1.5-fold, respectively. This study reports the discovery of a novel, multifunctional, and thermostable CarP from hot-spring metagenomes. The enzyme's stability against high temperatures, metal ions, surfactants, and inhibitors, along with its specific substrate interactions, highlights its potential for various biotechnological applications.
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Affiliation(s)
- Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar 144411, Punjab, India
| | - Chirag Chopra
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar 144411, Punjab, India
| | - Mushtaq Ahmad Ansari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mudasir A Dar
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, 212013, China
| | - Juliana Heloisa Pinê Américo-Pinheiro
- São Paulo State University (UNESP), School of Agricultural Sciences, Botucatu, Department of Forest Science, Soils and Environment, Ave. Universitária, 3780, Botucatu, SP 18610-034, Brazil; Graduate Program in Environmental Sciences, Brazil University, Street Carolina Fonseca, 584, São Paulo, SP 08230-030, Brazil.
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar 144411, Punjab, India.
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Sanderlin AG, Kurka Margolis H, Meyer AF, Lamason RL. Cell-selective proteomics reveal novel effectors secreted by an obligate intracellular bacterial pathogen. Nat Commun 2024; 15:6073. [PMID: 39025857 PMCID: PMC11258249 DOI: 10.1038/s41467-024-50493-9] [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: 11/27/2023] [Accepted: 07/11/2024] [Indexed: 07/20/2024] Open
Abstract
Pathogenic bacteria secrete protein effectors to hijack host machinery and remodel their infectious niche. Rickettsia spp. are obligate intracellular bacteria that can cause life-threatening disease, but their absolute dependence on the host cell has impeded discovery of rickettsial effectors and their host targets. We implemented bioorthogonal non-canonical amino acid tagging (BONCAT) during R. parkeri infection to selectively label, isolate, and identify effectors delivered into the host cell. As the first use of BONCAT in an obligate intracellular bacterium, our screen more than doubles the number of experimentally validated effectors for the genus. The seven novel secreted rickettsial factors (Srfs) we identified include Rickettsia-specific proteins of unknown function that localize to the host cytoplasm, mitochondria, and ER. We further show that one such effector, SrfD, interacts with the host Sec61 translocon. Altogether, our work uncovers a diverse set of previously uncharacterized rickettsial effectors and lays the foundation for a deeper exploration of the host-pathogen interface.
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Affiliation(s)
- Allen G Sanderlin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Abigail F Meyer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rebecca L Lamason
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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49
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Chand Y, Jain T, Singh S. Unveiling a Comprehensive Multi-epitope Subunit Vaccine Strategy Against Salmonella subsp. enterica: Bridging Core, Subtractive Proteomics, and Immunoinformatics. Cell Biochem Biophys 2024:10.1007/s12013-024-01407-5. [PMID: 39018007 DOI: 10.1007/s12013-024-01407-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2024] [Indexed: 07/18/2024]
Abstract
Salmonella subsp. enterica (SE) presents a significant global health challenge in both developed and developing countries. Current SE vaccines have limitations, targeting specific strains and demonstrating moderate efficacy in adults, while also being unsuitable for young children and often unaffordable in regions with lower income levels where the disease is prevalent. To address these challenges, this study employed a computational approach integrating core proteomics, subtractive proteomics, and immunoinformatics to develop a universal SE vaccine and identify potential drug targets. Analysis of the core proteome of 185 SE strains revealed 1964 conserved proteins. Subtractive proteomics identified 9 proteins as potential vaccine candidates and 41 as novel drug targets. Using reverse vaccinology-based immunoinformatics, four multi-epitope-based subunit vaccine constructs (MESVCs) were designed, aiming to stimulate cytotoxic T lymphocyte, helper T lymphocyte, and linear B lymphocyte responses. These constructs underwent comprehensive evaluations for antigenicity, immunogenicity, toxicity, hydropathicity, and physicochemical properties. Predictive modeling, refinement, and validation were conducted to determine the secondary and tertiary structures of the SE-MESVCs, followed by docking studies with MHC-I, MHC-II, and TLR4 receptors. Molecular docking assessments showed favorable binding with all three receptors, with SE-MESVC-4 exhibiting the most promising binding energy. Molecular dynamics simulations confirmed the binding affinity and stability of SE-MESVC-4 with the TLR4/MD2 complex. Additionally, codon optimization and in silico cloning verified the efficient translation and successful expression of SE-MESVC-4 in Escherichia coli (E. coli) str. K12. Subsequent in silico immune simulation evaluated the efficacy of SE-MESVC-4 in triggering an effective immune response. These results suggest that SE-MESVC-4 may induce both humoral and cellular immune responses, making it a potential candidate for an effective SE vaccine. However, further experimental investigations are necessary to validate the immunogenicity and efficacy of SE-MESVC-4, bringing us closer to effectively combating SE infections.
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Affiliation(s)
- Yamini Chand
- Faculty of Biotechnology, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, 225003, Uttar Pradesh, India
| | - Tanvi Jain
- Faculty of Biotechnology, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, 225003, Uttar Pradesh, India
| | - Sachidanand Singh
- Department of Biotechnology, School of Energy and Technology, Pandit Deendayal Energy University, Gandhinagar, 382426, Gujarat, India.
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50
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Kataria A, Srivastava A, Singh DD, Haque S, Han I, Yadav DK. Systematic computational strategies for identifying protein targets and lead discovery. RSC Med Chem 2024; 15:2254-2269. [PMID: 39026640 PMCID: PMC11253860 DOI: 10.1039/d4md00223g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/10/2024] [Indexed: 07/20/2024] Open
Abstract
Computational algorithms and tools have retrenched the drug discovery and development timeline. The applicability of computational approaches has gained immense relevance owing to the dramatic surge in the structural information of biomacromolecules and their heteromolecular complexes. Computational methods are now extensively used in identifying new protein targets, druggability assessment, pharmacophore mapping, molecular docking, the virtual screening of lead molecules, bioactivity prediction, molecular dynamics of protein-ligand complexes, affinity prediction, and for designing better ligands. Herein, we provide an overview of salient components of recently reported computational drug-discovery workflows that includes algorithms, tools, and databases for protein target identification and optimized ligand selection.
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Affiliation(s)
- Arti Kataria
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) Hamilton MT 59840 USA
| | - Ankit Srivastava
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) Hamilton MT 59840 USA
| | - Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan Jaipur India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Health Sciences, Jazan University Jazan-45142 Saudi Arabia
| | - Ihn Han
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University Seoul 01897 Republic of Korea +82 32 820 4948
| | - Dharmendra Kumar Yadav
- Department of Biologics, College of Pharmacy, Gachon University Hambakmoeiro 191, Yeonsu-gu Incheon 21924 Republic of Korea
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