1
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Butterfield ER, Obado SO, Scutts SR, Zhang W, Chait BT, Rout MP, Field MC. A lineage-specific protein network at the trypanosome nuclear envelope. Nucleus 2024; 15:2310452. [PMID: 38605598 PMCID: PMC11018031 DOI: 10.1080/19491034.2024.2310452] [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: 10/19/2023] [Accepted: 01/18/2024] [Indexed: 04/13/2024] Open
Abstract
The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization and nucleocytoplasmic transport. The molecular basis for many of these functions have diverged between eukaryotic lineages. Trypanosoma brucei, a member of the early branching eukaryotic lineage Discoba, highlights many of these, including a distinct lamina and kinetochore composition. Here, we describe a cohort of proteins interacting with both the lamina and NPC, which we term lamina-associated proteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with S. cerevisiae and H. sapiens, and additional peripheral components of the NPC. While many of the LAPs are Kinetoplastid specific, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the trypanosome NE proteome, highlighting the diversity of nuclear biology across the eukaryotes, increasing our understanding of eukaryotic and NPC evolution.
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Affiliation(s)
| | - Samson O. Obado
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Simon R. Scutts
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Mark C. Field
- School of Life Sciences, University of Dundee, Dundee, UK
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic
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2
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Li M, Qing R, Tao F, Xu P, Zhang S. Inhibitory effect of truncated isoforms on GPCR dimerization predicted by combinatorial computational strategy. Comput Struct Biotechnol J 2024; 23:278-286. [PMID: 38173876 PMCID: PMC10762321 DOI: 10.1016/j.csbj.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
G protein-coupled receptors (GPCRs) play a pivotal role in fundamental biological processes and disease development. GPCR isoforms, derived from alternative splicing, can exhibit distinct signaling patterns. Some highly-truncated isoforms can impact functional performance of full-length receptors, suggesting their intriguing regulatory roles. However, how these truncated isoforms interact with full-length counterparts remains largely unexplored. Here, we computationally investigated the interaction patterns of three human GPCRs from three different classes, ADORA1 (Class A), mGlu2 (Class C) and SMO (Class F) with their respective truncated isoforms because their homodimer structures have been experimentally determined, and they have truncated isoforms deposited and identified at protein level in Uniprot database. Combining the neural network-based AlphaFold2 and two physics-based protein-protein docking tools, we generated multiple complex structures and assessed the binding affinity in the context of atomistic molecular dynamics simulations. Our computational results suggested all the four studied truncated isoforms showed potent binding to their counterparts and overlapping interfaces with homodimers, indicating their strong potential to block homodimerization of their counterparts. Our study offers insights into functional significance of GPCR truncated isoforms and supports the ubiquity of their regulatory roles.
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Affiliation(s)
- Mengke Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rui Qing
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuguang Zhang
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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3
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Zeng S, Wang D, Jiang L, Xu D. Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction. Genome Res 2024; 34:1445-1454. [PMID: 39060029 DOI: 10.1101/gr.279132.124] [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: 02/15/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024]
Abstract
Signal peptides (SPs) play a crucial role in protein translocation in cells. The development of large protein language models (PLMs) and prompt-based learning provide a new opportunity for SP prediction, especially for the categories with limited annotated data. We present a parameter-efficient fine-tuning (PEFT) framework for SP prediction, PEFT-SP, to effectively utilize pretrained PLMs. We integrated low-rank adaptation (LoRA) into ESM-2 models to better leverage the protein sequence evolutionary knowledge of PLMs. Experiments show that PEFT-SP using LoRA enhances state-of-the-art results, leading to a maximum Matthews correlation coefficient (MCC) gain of 87.3% for SPs with small training samples and an overall MCC gain of 6.1%. Furthermore, we also employed two other PEFT methods, prompt tuning and adapter tuning, in ESM-2 for SP prediction. More elaborate experiments show that PEFT-SP using adapter tuning can also improve the state-of-the-art results by up to 28.1% MCC gain for SPs with small training samples and an overall MCC gain of 3.8%. LoRA requires fewer computing resources and less memory than the adapter tuning during the training stage, making it possible to adapt larger and more powerful protein models for SP prediction.
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Affiliation(s)
- Shuai Zeng
- Department of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Duolin Wang
- Department of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Lei Jiang
- Department of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
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4
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Chu X, Wang L, Zhu Y, Feng Z, Guan Q, Song L, Luo Z. A unique cell division protein critical for the assembly of the bacterial divisome. eLife 2024; 12:RP87922. [PMID: 39361022 PMCID: PMC11449484 DOI: 10.7554/elife.87922] [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] [Indexed: 10/05/2024] Open
Abstract
Identification of unique essential bacterial genes is important for not only the understanding of their cell biology but also the development of new antimicrobials. Here, we report a previously unrecognized core component of the Acinetobacter baumannii divisome. Our results reveal that the protein, termed Aeg1 interacts with multiple cell division proteins, including FtsN, which is required for components of the divisome to localize to the midcell. We demonstrate that the FtsAE202K and FtsBE65A mutants effectively bypassed the need of Aeg1 by A. baumannii, as did the activation variants FtsWM254I and FtsWS274G. Our results suggest that Aeg1 is a cell division protein that arrives at the division site to initiate cell division by recruiting FtsN, which activates FtsQLB and FtsA to induce the septal peptidoglycan synthase FtsWI. The discovery of the new essential cell division protein has provided a new target for the development of antibacterial agents.
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Affiliation(s)
- Xiao Chu
- Department of Respiratory Medicine, Infectious Diseases and Pathogen Biology Center State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Lidong Wang
- Department of Respiratory Medicine, Infectious Diseases and Pathogen Biology Center State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Yiheng Zhu
- Department of Respiratory Medicine, Infectious Diseases and Pathogen Biology Center State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Zhengshan Feng
- Department of Respiratory Medicine, Infectious Diseases and Pathogen Biology Center State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Qingtian Guan
- Bioinformatics Laboratory, The First Hospital of Jilin University, Changchun, China
| | - Lei Song
- Department of Respiratory Medicine, Infectious Diseases and Pathogen Biology Center State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Zhaoqing Luo
- Department of Respiratory Medicine, Infectious Diseases and Pathogen Biology Center State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
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5
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Li H, Khan IU, Anarjan MB, Hussain M, Lee S. The mutant STAY-GREEN ( Cssgr) in cucumber interacts with the CSEP30 protein to elicit a defense response against Podosphaera xanthii. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:67. [PMID: 39345972 PMCID: PMC11436540 DOI: 10.1007/s11032-024-01504-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 09/15/2024] [Indexed: 10/01/2024]
Abstract
Disease-resistant plants activate immune responses by specifically recognition Candidate Secreted Effector Proteins (CSEPs) through resistance (R) proteins. In research on cucumber powdery mildew resistance breeding, several R genes and CSEPs have been identified; however, the specific interactions between R proteins and CSEPs are still largely unexplored. In this study, we used a luciferase reporter assay to identify six CSEPs from Podosphaera xanthii that potentially induce cell death in cucumber. Subsequent yeast two-hybrid analysis revealed that only the mature form of CSEP30 (CSEP30∆SP) interacted with the cucumber mutant STAY-GREEN (Cssgr), a gene previously recognized for its broad-spectrum resistance in genetic studies. This interaction was confirmed using pull-down and co-immunoprecipitation assays. Additionally, to determine if the interaction leads to phenotypic changes, Cssgr and CSEP30∆SP were transiently expressed in tobacco leaves. The infiltration of Cssgr in tobacco resulted in reduced chlorosis compared to the wild-type CsSGR. Co-infiltration of Cssgr with CSEP30∆SP induced distinct dry necrotic lesions, contrasting the effects observed when Cssgr and CSEP30∆SP were infiltrated separately. Additionally, after P. xanthii infection in moderately powdery mildew-resistant Gy14 cucumber, similar necrotic lesions and specific expression of Cssgr, as along with defense response-related genes (CsPR1 and CsLecRK6.1), were observed. This study suggests that the interaction between Cssgr and CSEP30∆SP could trigger cell death and defense response, offering new insights into the molecular function of Cssgr in disease resistance in Gy14 cucumber. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01504-6.
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Affiliation(s)
- Haisu Li
- Plant Genomics Laboratory, Department of Bio-Resource Engineering, College of Life Sciences, Sejong University, Room 409B Kwanggaetokwan, 209 Neungdong-Ro, Gwanjing-Gu, Seoul, 05006 Republic of Korea
| | - Irfan Ullah Khan
- Plant Genomics Laboratory, Department of Bio-Resource Engineering, College of Life Sciences, Sejong University, Room 409B Kwanggaetokwan, 209 Neungdong-Ro, Gwanjing-Gu, Seoul, 05006 Republic of Korea
| | - Mahdi Badri Anarjan
- Plant Genomics Laboratory, Department of Bio-Resource Engineering, College of Life Sciences, Sejong University, Room 409B Kwanggaetokwan, 209 Neungdong-Ro, Gwanjing-Gu, Seoul, 05006 Republic of Korea
| | - Muhammad Hussain
- Plant Genomics Laboratory, Department of Bio-Resource Engineering, College of Life Sciences, Sejong University, Room 409B Kwanggaetokwan, 209 Neungdong-Ro, Gwanjing-Gu, Seoul, 05006 Republic of Korea
| | - Sanghyeob Lee
- Plant Genomics Laboratory, Department of Bio-Resource Engineering, College of Life Sciences, Sejong University, Room 409B Kwanggaetokwan, 209 Neungdong-Ro, Gwanjing-Gu, Seoul, 05006 Republic of Korea
- Plant Engineering Research Institute, Sejong University, 209 Neungdong-Ro, Gwanjing-Gu, Seoul, 05006 Republic of Korea
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6
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Zhou X, Khan MF, Xin Y, Chan KL, Roujeinikova A. Biochemical characterization of paralyzed flagellum proteins A (PflA) and B (PflB) from Helicobacter pylori flagellar motor. Biosci Rep 2024; 44:BSR20240692. [PMID: 39105472 PMCID: PMC11392913 DOI: 10.1042/bsr20240692] [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: 05/30/2024] [Revised: 07/29/2024] [Accepted: 08/06/2024] [Indexed: 08/07/2024] Open
Abstract
Motility by means of flagella plays an important role in the persistent colonization of Helicobacter pylori in the human stomach. The H. pylori flagellar motor has a complex structure that includes a periplasmic scaffold, the components of which are still being identified. Here, we report the isolation and characterization of the soluble forms of two putative essential H. pylori motor scaffold components, proteins PflA and PflB. We developed an on-column refolding procedure, overcoming the challenge of inclusion body formation in Escherichia coli. We employed mild detergent sarkosyl to enhance protein recovery and n-dodecyl-N,N-dimethylamine-N-oxide (LDAO)-containing buffers to achieve optimal solubility and monodispersity. In addition, we showed that PflA lacking the β-rich N-terminal domain is expressed in a soluble form, and behaves as a monodisperse monomer in solution. The methods for producing the soluble, folded forms of H. pylori PflA and PflB established in this work will facilitate future biophysical and structural studies aimed at deciphering their location and their function within the flagellar motor.
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Affiliation(s)
- Xiaotian Zhou
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria 3800, Australia
| | - Muhammad F Khan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria 3800, Australia
| | - Yue Xin
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria 3800, Australia
| | - Kar L Chan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria 3800, Australia
| | - Anna Roujeinikova
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
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7
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Deepika, Madhu, Shekhawat J, Dixit S, Upadhyay SK. Pre-mRNA processing factor 4 kinases (PRP4Ks): Exploration of molecular features, interaction network and expression profiling in bread wheat. JOURNAL OF PLANT GROWTH REGULATION 2024. [DOI: 10.1007/s00344-024-11489-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 09/06/2024] [Indexed: 10/09/2024]
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8
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Lee PJ, Sun Y, Soares AR, Fai C, Picciotto MR, Guo JU. Alternative translation initiation produces synaptic organizer proteoforms with distinct localization and functions. Mol Cell 2024:S1097-2765(24)00728-7. [PMID: 39317199 DOI: 10.1016/j.molcel.2024.08.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 07/03/2024] [Accepted: 08/29/2024] [Indexed: 09/26/2024]
Abstract
While many mRNAs contain more than one translation initiation site (TIS), the functions of most alternative TISs and their corresponding protein isoforms (proteoforms) remain undetermined. Here, we showed that alternative usage of CUG and AUG TISs in neuronal pentraxin receptor (NPR) mRNA produced two proteoforms, of which the ratio was regulated by RNA secondary structure and neuronal activity. Downstream AUG initiation truncated the N-terminal transmembrane domain and produced a secreted NPR proteoform sufficient in promoting synaptic clustering of AMPA-type glutamate receptors. Mutations that altered the ratio of NPR proteoforms reduced AMPA receptors in parvalbumin-positive interneurons and affected learning behaviors in mice. In addition to NPR, upstream AUU-initiated N-terminal extension of C1q-like synaptic organizers anchored these otherwise secreted factors to the membrane. Together, these results uncovered the plasticity of N-terminal signal sequences regulated by alternative TIS usage as a potentially widespread mechanism in diversifying protein localization and functions.
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Affiliation(s)
- Paul Jongseo Lee
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Yu Sun
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Alexa R Soares
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06508, USA; Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Caroline Fai
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06508, USA
| | - Marina R Picciotto
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06508, USA; Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Junjie U Guo
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA.
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9
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Tajuelo A, Gato E, Oteo-Iglesias J, Pérez-Vázquez M, McConnell MJ, Martín-Galiano AJ, Pérez A. Deep Intraclonal Analysis for the Development of Vaccines against Drug-Resistant Klebsiella pneumoniae Lineages. Int J Mol Sci 2024; 25:9837. [PMID: 39337325 PMCID: PMC11431857 DOI: 10.3390/ijms25189837] [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: 08/20/2024] [Revised: 09/05/2024] [Accepted: 09/08/2024] [Indexed: 09/30/2024] Open
Abstract
Despite its medical relevance, there is no commercial vaccine that protects the population at risk from multidrug-resistant (MDR) Klebsiella pneumoniae infections. The availability of massive omic data and novel algorithms may improve antigen selection to develop effective prophylactic strategies. Up to 133 exposed proteins in the core proteomes, between 516 and 8666 genome samples, of the six most relevant MDR clonal groups (CGs) carried conserved B-cell epitopes, suggesting minimized future evasion if utilized for vaccination. Antigens showed a range of epitopicity, functional constraints, and potential side effects. Eleven antigens, including three sugar porins, were represented in all MDR-CGs, constitutively expressed, and showed limited reactivity with gut microbiota. Some of these antigens had important interactomic interactions and may elicit adhesion-neutralizing antibodies. Synergistic bivalent to pentavalent combinations that address expression conditions, interactome location, virulence activities, and clone-specific proteins may overcome the limiting protection of univalent vaccines. The combination of five central antigens accounted for 41% of all non-redundant interacting partners of the antigen dataset. Specific antigen mixtures represented in a few or just one MDR-CG further reduced the chance of microbiota interference. Rational antigen selection schemes facilitate the design of high-coverage and "magic bullet" multivalent vaccines against recalcitrant K. pneumoniae lineages.
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Affiliation(s)
- Ana Tajuelo
- Intrahospital Infections Unit, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28220 Madrid, Spain
- Universidad Nacional de Educación a Distancia (UNED), 28015 Madrid, Spain
| | - Eva Gato
- Intrahospital Infections Unit, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28220 Madrid, Spain
| | - Jesús Oteo-Iglesias
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28220 Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - María Pérez-Vázquez
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28220 Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Michael J McConnell
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Antonio J Martín-Galiano
- Core Scientific and Technical Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28220 Madrid, Spain
| | - Astrid Pérez
- Intrahospital Infections Unit, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28220 Madrid, Spain
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Wasmund K, Singleton C, Dahl Dueholm MK, Wagner M, Nielsen PH. The predicted secreted proteome of activated sludge microorganisms indicates distinct nutrient niches. mSystems 2024:e0030124. [PMID: 39254351 DOI: 10.1128/msystems.00301-24] [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: 02/27/2024] [Accepted: 08/08/2024] [Indexed: 09/11/2024] Open
Abstract
In wastewater treatment plants (WWTPs), complex microbial communities process diverse chemical compounds from sewage. Secreted proteins are critical because many are the first to interact with or degrade external (macro)molecules. To better understand microbial functions in WWTPs, we predicted secreted proteomes of WWTP microbiota from more than 1,000 high-quality metagenome-assembled genomes (MAGs) from 23 Danish WWTPs with biological nutrient removal. Focus was placed on examining secreted catabolic exoenzymes that target major classes of macromolecules. We demonstrate that Bacteroidota has a high potential to digest complex polysaccharides, but also proteins and nucleic acids. Poorly understood activated sludge members of Acidobacteriota and Gemmatimonadota also have high capacities for extracellular polysaccharide digestion. Secreted nucleases are encoded by 61% of MAGs indicating an importance for extracellular DNA and/or RNA digestion in WWTPs. Secreted lipases were the least common macromolecule-targeting enzymes predicted, encoded mainly by Gammaproteobacteria and Myxococcota. In contrast, diverse taxa encode extracellular peptidases, indicating that proteins are widely used nutrients. Diverse secreted multi-heme cytochromes suggest capabilities for extracellular electron transfer by various taxa, including some Bacteroidota that encode undescribed cytochromes with >100 heme-binding motifs. Myxococcota have exceptionally large secreted protein complements, probably related to predatory lifestyles and/or complex cell cycles. Many Gammaproteobacteria MAGs (mostly former Betaproteobacteria) encode few or no secreted hydrolases, but many periplasmic substrate-binding proteins and ABC- and TRAP-transporters, suggesting they are mostly sustained by small molecules. Together, this study provides a comprehensive overview of how WWTPs microorganisms interact with the environment, providing new insights into their functioning and niche partitioning.IMPORTANCEWastewater treatment plants (WWTPs) are critical biotechnological systems that clean wastewater, allowing the water to reenter the environment and limit eutrophication and pollution. They are also increasingly important for the recovery of resources. They function primarily by the activity of microorganisms, which act as a "living sponge," taking up and transforming nutrients, organic material, and pollutants. Despite much research, many microorganisms in WWTPs are uncultivated and poorly characterized, limiting our understanding of their functioning. Here, we analyzed a large collection of high-quality metagenome-assembled genomes from WWTPs for encoded secreted enzymes and proteins, with special emphasis on those used to degrade organic material. This analysis showed highly distinct secreted proteome profiles among different major phylogenetic groups of microorganisms, thereby providing new insights into how different groups function and co-exist in activated sludge. This knowledge will contribute to a better understanding of how to efficiently manage and exploit WWTP microbiomes.
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Affiliation(s)
- Kenneth Wasmund
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- School of Biological Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Caitlin Singleton
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Kam Dahl Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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11
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Li Q, Liu F, Ma X, Chen F, Yi Z, Du Y, Huang A, Zhao C, Wang D, Chen Y, Cao X. Proteomic Profiling of Unannotated Microproteins in Human Placenta Reveals XRCC6P1 as a Potential Negative Regulator of Translation. J Proteome Res 2024; 23:4005-4013. [PMID: 39171377 DOI: 10.1021/acs.jproteome.4c00319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Ribosome profiling and mass spectrometry have revealed thousands of previously unannotated small and alternative open reading frames (sm/alt-ORFs) that are translated into micro/alt-proteins in mammalian cells. However, their prevalence across human tissues and biological roles remains largely undefined. The placenta is an ideal model for identifying unannotated microproteins and alt-proteins due to its considerable protein diversity that is required to sustain fetal development during pregnancy. Here, we profiled unannotated microproteins and alt-proteins in human placental tissues from preeclampsia patients or healthy individuals by proteomics, identified 52 unannotated microproteins or alt-proteins, and demonstrated that five microproteins can be translated from overexpression constructs in a heterologous cell line, although several are unstable. We further demonstrated that one microprotein, XRCC6P1, associates with translation initiation factor eIF3 and negatively regulates translation when exogenously overexpressed. Thus, we revealed a hidden sm/alt-ORF-encoded proteome in the human placenta, which may advance the mechanism studies for placenta development as well as placental disorders such as preeclampsia.
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Affiliation(s)
- Qiong Li
- Department of Obstetrics and Gynecology, The First People's Hospital of Chenzhou, Chenzhou 423000, China
- The First Affiliated Hospital of Jinan University, Guangzhou 510632, China
| | - Fanrong Liu
- Department of Orthopedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Xiaoyu Ma
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Feifei Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Ziying Yi
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yangyang Du
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Anxin Huang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Chenyang Zhao
- Department of Obstetrics and Gynecology, The First People's Hospital of Chenzhou, Chenzhou 423000, China
- The First Affiliated Hospital of Jinan University, Guangzhou 510632, China
| | - Da Wang
- Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Navy Military Medical University, Shanghai 200003, China
| | - Yanran Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xiongwen Cao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
- Key Laboratory of Brain Functional Genomics, Ministry of Education and Shanghai, School of Life Sciences, East China Normal University, Shanghai 200062, China
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12
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Ungri AM, Dos Santos Sabatke BF, Rossi IV, das Neves GB, Marques J, Ribeiro BG, Borges GK, Moreira RS, Ramírez MI, Miletti LC. Extracellular vesicles released by Trypanosoma evansi: induction analysis and proteomics. Parasitol Res 2024; 123:314. [PMID: 39225716 DOI: 10.1007/s00436-024-08330-x] [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: 05/27/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
Trypanosoma evansi is a unicellular protozoan responsible for causing a disease known as "surra," which is found in different regions of the world and primarily affects horses and camels. Few information is known about virulence factors released from the parasite within the animals. The organism can secrete extracellular vesicles (EVs), which transport a variety of molecules, including proteins. Before being considered exclusively as a means for eliminating unwanted substances, extracellular vesicles (EVs) have emerged as key players in intercellular communication, facilitating interactions between cells, host cells, and parasites, and even between parasites themselves. Thus, they may be used as potential biomarkers. This study aimed to assess the induction of EVs production by Ca+2, conduct a proteomic analysis of the EVs released by T. evansi, and identify epitopes that could serve as biomarkers. The findings indicated that Ca+2 is not an effective promoter of vesiculation in T. evansi. Furthermore, the proteomic analysis has identified multiple proteins that have been investigated as biomarkers or vaccine antigens, previously. A total of 442 proteins were identified, with 7 of them specifically recognizing 9 epitopes that are unique to T. evansi. At least one of these epitopes of TevSTIB805.9.11580 have been previously identified, which increases the possibility of further investigating its potential as a biomarker.
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Affiliation(s)
- Amanda Martins Ungri
- Laboratório de Hemoparasitas E Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade Do Estado de Santa Catarina (UDESC), Av. Luiz de Camões, 2090, Conta Dinheiro, Lages, 88520-000, SC, Brazil
| | - Bruna Fernanda Dos Santos Sabatke
- Laboratório de Biologia Celular, EVAHPI-Extracellular Vesicles and Host-Parasite Interactions Research Group, Instituto Carlos Chagas-Fiocruz, Curitiba, 81310-020, Brazil
| | - Izadora Volpato Rossi
- Laboratório de Biologia Celular, EVAHPI-Extracellular Vesicles and Host-Parasite Interactions Research Group, Instituto Carlos Chagas-Fiocruz, Curitiba, 81310-020, Brazil
| | - Gabriella Bassi das Neves
- Laboratório de Hemoparasitas E Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade Do Estado de Santa Catarina (UDESC), Av. Luiz de Camões, 2090, Conta Dinheiro, Lages, 88520-000, SC, Brazil
| | - Júlia Marques
- Laboratório de Hemoparasitas E Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade Do Estado de Santa Catarina (UDESC), Av. Luiz de Camões, 2090, Conta Dinheiro, Lages, 88520-000, SC, Brazil
| | - Brenda Guedes Ribeiro
- Laboratório de Hemoparasitas E Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade Do Estado de Santa Catarina (UDESC), Av. Luiz de Camões, 2090, Conta Dinheiro, Lages, 88520-000, SC, Brazil
| | - Gabriela Kaiser Borges
- Laboratório de Hemoparasitas E Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade Do Estado de Santa Catarina (UDESC), Av. Luiz de Camões, 2090, Conta Dinheiro, Lages, 88520-000, SC, Brazil
| | - Renato Simões Moreira
- Instituto Federal de Santa Catarina (IFSC), Campus Gaspar, R. Adriano Kormann, 510-Bela Vista, Gaspar, SC, Brazil
| | - Marcel Ivan Ramírez
- Laboratório de Biologia Celular, EVAHPI-Extracellular Vesicles and Host-Parasite Interactions Research Group, Instituto Carlos Chagas-Fiocruz, Curitiba, 81310-020, Brazil
| | - Luiz Claudio Miletti
- Laboratório de Hemoparasitas E Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade Do Estado de Santa Catarina (UDESC), Av. Luiz de Camões, 2090, Conta Dinheiro, Lages, 88520-000, SC, Brazil.
- Departamento de Produção Animal E Alimentos, Centro de Ciências Agroveterinárias, Universidade Do Estado de Santa Catarina, Av. Luiz de Camões, 2090 Bairro Conta Dinheiro, Lages, SC, 88520-000, Brazil.
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13
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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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14
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Mursaleen S, Sarfraz A, Shehroz M, Zaman A, Rahman FU, Moura AA, Sheheryar S, Aziz S, Ullah R, Iqbal Z, Nishan U, Shah M, Sun W. Genome-level therapeutic targets identification and chimeric Vaccine designing against the Blastomyces dermatitidis. Heliyon 2024; 10:e36153. [PMID: 39224264 PMCID: PMC11367477 DOI: 10.1016/j.heliyon.2024.e36153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 08/11/2024] [Indexed: 09/04/2024] Open
Abstract
Blastomyces dermatitidis is a thermally dimorphic fungus that can cause serious and sometimes fatal infections, including blastomycosis. After spore inhalation, a pulmonary infection develops, which can be asymptomatic and have lethal effects, such as acute respiratory distress syndrome. Its most common extra-pulmonary sites are the central nervous system, bones, skin, and genito-urinary systems. Currently, no vaccine has been approved by the FDA to prevent this infection. In the study, a peptide-based vaccine was developed against blastomycosis by using subtractive proteomics and reverse vaccinology approaches. It focuses on mining the whole genome of B. dermatitidis, identifying potential therapeutic targets, and pinpointing potential epitopes for both B- and T-cells that are immunogenic, non-allergenic, non-toxic, and highly antigenic. Multi-epitope constructs were generated by incorporating appropriate linker sequences. A linker (EAAAK) was also added to incorporate an adjuvant sequence to increase immunological potential. The addition of adjuvants and linkers ultimately resulted in the formation of a vaccine construct in which the number of amino acids was 243 and the molecular weight was 26.18 kDa. The designed antigenic and non-allergenic vaccine constructs showed suitable physicochemical properties. The vaccine's structures were predicted, and further analysis verified their interactions with the human TLR-4 receptor through protein-protein docking. Additionally, MD simulation showed a potent interaction between prioritized vaccine-receptor complexes. Immune simulation predicted that the final vaccine injections resulted in significant immune responses for the T- and B-cell immune responses. Moreover, in silico cloning ensured a high expression possibility of the lead vaccine in the E. coli (K12) vector. This study offers an initiative for the development of effective vaccines against B. dermatitidis; however, it is necessary to validate the designed vaccine's immunogenicity experimentally.
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Affiliation(s)
- Sawvara Mursaleen
- Department of Biochemistry, Bahauddin Zakariya University, Multan-66000, Pakistan
| | - Asifa Sarfraz
- Department of Biochemistry, Bahauddin Zakariya University, Multan-66000, Pakistan
| | - Muhammad Shehroz
- Department of Bioinformatics, Kohsar University Murree, Murree-47150, Pakistan
| | - Aqal Zaman
- Department of Microbiology & Molecular Genetics, Bahauddin Zakariya University, Multan-66000, Pakistan
| | - Faiz U Rahman
- Department of Zoology, Shangla Campus, University of Swat, Khyber Pakhtunkhwa, Pakistan
| | - Arlindo A. Moura
- Department of Animal Science, Federal University of Ceara, Fortaleza, Brazil
| | - Sheheryar Sheheryar
- Department of Animal Science, Federal University of Ceara, Fortaleza, Brazil
| | - Shahid Aziz
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60451-970, Brazil
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University Riyadh Saudi Arabia, Kingdom of Saudi Arabia
| | - Zafar Iqbal
- Department of Surgery, College of Medicine, King Saud University P.O. Box 7805, Riyadh, 11472, Kingdom of Saudi Arabia
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan-66000, Pakistan
| | - Wenwen Sun
- Department of Intensive Care Unit, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 213004, China
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15
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Hashempour A, Khodadad N, Akbarinia S, Ghasabi F, Ghasemi Y, Nazar MMKA, Falahi S. Reverse vaccinology approaches to design a potent multiepitope vaccine against the HIV whole genome: immunoinformatic, bioinformatics, and molecular dynamics approaches. BMC Infect Dis 2024; 24:873. [PMID: 39198721 PMCID: PMC11360854 DOI: 10.1186/s12879-024-09775-2] [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: 01/09/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024] Open
Abstract
Substantial advances have been made in the development of promising HIV vaccines to eliminate HIV-1 infection. For the first time, one hundred of the most submitted HIV subtypes and CRFs were retrieved from the LANL database, and the consensus sequences of the eleven HIV proteins were obtained to design vaccines for human and mouse hosts. By using various servers and filters, highly qualified B-cell epitopes, as well as HTL and CD8 + epitopes that were common between mouse and human alleles and were also located in the conserved domains of HIV proteins, were considered in the vaccine constructs. With 90% coverage worldwide, the human vaccine model covers a diverse allelic population, making it widely available. Codon optimization and in silico cloning in prokaryotic and eukaryotic vectors guarantee high expression of the vaccine models in human and E. coli hosts. Molecular dynamics confirmed the stable interaction of the vaccine constructs with TLR3, TLR4, and TLR9, leading to a substantial immunogenic response to the designed vaccine. Vaccine models effectively target the humoral and cellular immune systems in humans and mice; however, experimental validation is needed to confirm these findings in silico.
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Affiliation(s)
- Ava Hashempour
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nastaran Khodadad
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Shokufeh Akbarinia
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farzane Ghasabi
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Shahab Falahi
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran.
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16
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Awad MM, Suraweera CD, Vidor CJ, Ye-Lin AY, Williams GC, Mileto SJ, Barlow CK, McGowan S, Lyras D. A Clostridioides difficile endolysin modulates toxin secretion without cell lysis. Commun Biol 2024; 7:1044. [PMID: 39179651 PMCID: PMC11344133 DOI: 10.1038/s42003-024-06730-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 08/13/2024] [Indexed: 08/26/2024] Open
Abstract
The Clostridia produce and secrete Large Clostridial Glucosylating Toxins (LCGTs) responsible for disease symptoms, but the secretion mechanism is largely unknown. Recently, a holin-like protein was shown to be essential for toxin secretion. Holins, typically bacteriophage-specific proteins, are part of the holin-endo(lysin) system that releases phage progeny. To determine if the clostridia also use a lysin, we investigated two conserved putative lysins, M7404_01910 and M7404_02200, in the release of the LCGTs TcdA and TcdB from a Clostridioides difficile ribotype 027 strain, M7404. Sequence analysis and structural modelling indicates that both proteins are related to N-acetylmuramoyl-l-alanine amidases, similar to CD27L, a lysin from the C. difficile phage ΦCD27. Disruption of these genes reveal that only M7404_02200 contributes to toxin secretion and does so in a non-lytic fashion. Peptidoglycan hydrolysis assays show that recombinant M7404_02200 is an active peptidoglycan amidase, confirming its role in TcdA and TcdB secretion in C. difficile M7404.
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Affiliation(s)
- Milena M Awad
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Chathura D Suraweera
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Callum J Vidor
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Auberon Y Ye-Lin
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Galain C Williams
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Steven J Mileto
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Christopher K Barlow
- Department of Biochemistry, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
- Monash Proteomics & Metabolomics Platform, Monash University, Clayton, 3800, Australia
| | - Sheena McGowan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Dena Lyras
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia.
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17
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Sailer AL, Jevtic Z, Stoll B, Wörtz J, Sharma K, Urlaub H, Dyall-Smith M, Pfeiffer F, Marchfelder A, Lenz C. Iron starvation results in up-regulation of a probable Haloferax volcanii siderophore transporter. Front Microbiol 2024; 15:1422844. [PMID: 39206359 PMCID: PMC11349517 DOI: 10.3389/fmicb.2024.1422844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024] Open
Abstract
The response of the haloarchaeal model organism Haloferax volcanii to iron starvation was analyzed at the proteome level by data-independent acquisition mass spectrometry. Cells grown in minimal medium with normal iron levels were compared to those grown under low iron conditions, with samples being separated into membrane and cytoplasmic fractions in order to focus on import/export processes which are frequently associated with metal homeostasis. Iron starvation not only caused a severe retardation of growth but also altered the levels of many proteins. Using a comprehensive annotated spectral library and data-independent acquisition mass spectrometry (DIA-MS), we found that iron starvation resulted in significant changes to both the membrane and the soluble proteomes of Hfx. volcanii. The most affected protein is the RND family permease HVO_A0467, which is 44-fold enriched in cells grown under iron starvation. The gene HVO_A0467 can be deleted suggesting that it is not essential under standard conditions. Compared to wild type cells the deletion strain shows only slight changes in growth and cell morphologies show no differences. Molecular docking predictions indicated that HVO_A0467 may be an exporter of the siderophore schizokinen for which a potential biosynthesis cluster is encoded in the Hfx. volcanii genome. Together, these findings confirm the importance of iron for archaeal cells and suggest HVO_0467 as a siderophore exporter.
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Affiliation(s)
| | - Zivojin Jevtic
- Department of Biomedicine, University Children’s Hospital, University of Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | | | - Kundan Sharma
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics Group, Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Mike Dyall-Smith
- Computational Systems Biochemistry, Max Planck Institute for Biochemistry, Martinsried, Germany
- Veterinary Biosciences, Faculty of Science, Melbourne Veterinary School, University of Melbourne, Parkville, VIC, Australia
| | - Friedhelm Pfeiffer
- Biology II, Ulm University, Ulm, Germany
- Computational Systems Biochemistry, Max Planck Institute for Biochemistry, Martinsried, Germany
| | | | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics Group, Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
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18
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Schnabel E, Bashyal S, Corbett C, Kassaw T, Nowak S, Rosales-García RA, Noorai RE, Müller LM, Frugoli J. The Defective in Autoregulation (DAR) gene of Medicago truncatula encodes a protein involved in regulating nodulation and arbuscular mycorrhiza. BMC PLANT BIOLOGY 2024; 24:766. [PMID: 39123119 PMCID: PMC11316349 DOI: 10.1186/s12870-024-05479-6] [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: 04/11/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Legumes utilize a long-distance signaling feedback pathway, termed Autoregulation of Nodulation (AON), to regulate the establishment and maintenance of their symbiosis with rhizobia. Several proteins key to this pathway have been discovered, but the AON pathway is not completely understood. RESULTS We report a new hypernodulating mutant, defective in autoregulation, with disruption of a gene, DAR (Medtr2g450550/MtrunA17_Chr2g0304631), previously unknown to play a role in AON. The dar-1 mutant produces ten-fold more nodules than wild type, similar to AON mutants with disrupted SUNN gene function. As in sunn mutants, suppression of nodulation by CLE peptides MtCLE12 and MtCLE13 is abolished in dar. Furthermore, dar-1 also shows increased root length colonization by an arbuscular mycorrhizal fungus, suggesting a role for DAR in autoregulation of mycorrhizal symbiosis (AOM). However, unlike SUNN which functions in the shoot to control nodulation, DAR functions in the root. CONCLUSIONS DAR encodes a membrane protein that is a member of a small protein family in M. truncatula. Our results suggest that DAR could be involved in the subcellular transport of signals involved in symbiosis regulation, but it is not upregulated during symbiosis. DAR gene family members are also present in Arabidopsis, lycophytes, mosses, and microalgae, suggesting the AON and AOM may use pathway components common to other plants, even those that do not undergo either symbiosis.
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Affiliation(s)
- Elise Schnabel
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
| | - Sagar Bashyal
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- School of Biological Sciences, University of California San Diego, San Diego, CA, 92093, USA
| | - Cameron Corbett
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
- Present addresses: Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Tessema Kassaw
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
- Present addresses: Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Stephen Nowak
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
- Present addresses: Center for Technology Licensing, Cornell University, Ithaca, NY, 14850, USA
| | - Ramsés Alejandro Rosales-García
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
- Clemson University Genomics and Bioinformatics Facility, Clemson University, Clemson, SC, 29634, USA
| | - Rooksana E Noorai
- Clemson University Genomics and Bioinformatics Facility, Clemson University, Clemson, SC, 29634, USA
| | - Lena Maria Müller
- Department of Biology, University of Miami, Coral Gables, FL, 33124, USA
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Julia Frugoli
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA.
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19
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Witmer NH, McLendon JM, Stein CS, Yoon JY, Berezhnaya E, Elrod JW, London BL, Boudreau RL. Upstream alternative polyadenylation in SCN5A produces a short transcript isoform encoding a mitochondria-localized NaV1.5 N-terminal fragment that influences cardiomyocyte respiration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.607406. [PMID: 39211120 PMCID: PMC11360925 DOI: 10.1101/2024.08.09.607406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
SCN5A encodes the cardiac voltage-gated Na+ channel, NaV1.5, that initiates action potentials. SCN5A gene variants cause arrhythmias and increased heart failure risk. Mechanisms controlling NaV1.5 expression and activity are not fully understood. We recently found a well-conserved alternative polyadenylation (APA) signal downstream of the first SCN5A coding exon. This yields a SCN5A-short transcript isoform expressed in several species (e.g. human, pig, and cat), though rodents lack this upstream APA. Reanalysis of transcriptome-wide cardiac APA-seq and mRNA-seq data shows reductions in both upstream APA usage and short/full-length SCN5A mRNA ratios in failing hearts. Knock-in of the human SCN5A APA sequence into mice is sufficient to enable expression of SCN5A -short transcript, while significantly decreasing expression of full-length SCN5A mRNA. Notably, SCN5A -short transcript encodes a novel protein (NaV1.5-NT), composed of an N-terminus identical to NaV1.5 and a unique C-terminus derived from intronic sequence. AAV9 constructs were able to achieve stable NaV1.5-NT expression in mouse hearts, and western blot of human heart tissues showed bands co-migrating with NaV1.5-NT transgene-derived bands. NaV1.5-NT is predicted to contain a mitochondrial targeting sequence and localizes to mitochondria in cultured cardiomyocytes and in mouse hearts. NaV1.5-NT expression in cardiomyocytes led to elevations in basal oxygen consumption rate, ATP production, and mitochondrial ROS, while depleting NADH supply. Native PAGE analyses of mitochondria lysates revealed that NaV1.5-NT expression resulted in increased levels of disassembled complex V subunits and accumulation of complex I-containing supercomplexes. Overall, we discovered that APA-mediated regulation of SCN5A produces a short transcript encoding NaV1.5-NT. Our data support that NaV1.5-NT plays a multifaceted role in influencing mitochondrial physiology: 1) by increasing basal respiration likely through promoting complex V conformations that enhance proton leak, and 2) by increasing overall respiratory efficiency and NADH consumption by enhancing formation and/or stability of complex I-containing respiratory supercomplexes, though the specific molecular mechanisms underlying each of these remain unresolved.
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20
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Chiappa G, Fassio G, Modica MV, Oliverio M. Potential Ancestral Conoidean Toxins in the Venom Cocktail of the Carnivorous Snail Raphitoma purpurea (Montagu, 1803) (Neogastropoda: Raphitomidae). Toxins (Basel) 2024; 16:348. [PMID: 39195758 PMCID: PMC11359391 DOI: 10.3390/toxins16080348] [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: 07/12/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 08/29/2024] Open
Abstract
Venomous marine gastropods of the superfamily Conoidea possess a rich arsenal of toxins, including neuroactive toxins. Venom adaptations might have played a fundamental role in the radiation of conoideans; nevertheless, there is still no knowledge about the venom of the most diversified family of the group: Raphitomidae Bellardi, 1875. In this study, transcriptomes were produced from the carcase, salivary glands, and proximal and distal venom ducts of the northeastern Atlantic species Raphitoma purpurea (Montagu, 1803). Using a gut barcoding approach, we were also able to report, for the first time, molecular evidence of a vermivorous diet for the genus. Transcriptomic analyses revealed over a hundred putative venom components (PVC), including 69 neurotoxins. Twenty novel toxin families, including some with high levels of expansion, were discovered. No significant difference was observed between the distal and proximal venom duct secretions. Peptides related to cone snail toxins (Cerm06, Pgam02, and turritoxin) and other venom-related proteins (disulfide isomerase and elevenin) were retrieved from the salivary glands. These salivary venom components may constitute ancestral adaptations for venom production in conoideans. Although often neglected, salivary gland secretions are of extreme importance for understanding the evolutionary history of conoidean venom.
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Affiliation(s)
- Giacomo Chiappa
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Viale dell’Università 32, 00185 Rome, Italy; (G.F.); (M.O.)
| | - Giulia Fassio
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Viale dell’Università 32, 00185 Rome, Italy; (G.F.); (M.O.)
| | - Maria Vittoria Modica
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Via Gregorio Allegri 1, 00198 Rome, Italy;
| | - Marco Oliverio
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Viale dell’Università 32, 00185 Rome, Italy; (G.F.); (M.O.)
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21
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Upadhaya A, Upadhaya SGC, Brueggeman R. Identification of Candidate Avirulence and Virulence Genes Corresponding to Stem Rust ( Puccinia graminis f. sp. tritici) Resistance Genes in Wheat. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:635-649. [PMID: 38780476 DOI: 10.1094/mpmi-05-24-0056-r] [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: 05/25/2024]
Abstract
Stem rust, caused by the biotrophic fungal pathogen Puccinia graminis f. sp. tritici (Pgt), is an important disease of wheat. However, the majority of Pgt virulence/avirulence loci and underlying genes remain uncharacterized due to the constraints of developing bi-parental populations with this obligate biotroph. Genome-wide association studies (GWAS) using a sexual Pgt population mainly collected from the Pacific Northwestern United States were used to identify candidate virulence/avirulence effector genes corresponding to the six wheat Sr genes: Sr5, Sr21, Sr8a, Sr17, Sr9a, and Sr9d. The Pgt isolates were genotyped using whole-genome shotgun sequencing that identified approximately 1.2 million single nucleotide polymorphisms (SNPs) and were phenotyped at the seedling stage on six Sr gene differential lines. Association mapping analyses identified 17 Pgt loci associated with virulence or avirulence phenotypes on six Pgt resistance genes. Among these loci, 16 interacted with a specific Sr gene, indicating Sr-gene specific interactions. However, one avirulence locus interacted with two separate Sr genes (Sr9a and Sr17), suggesting two distinct Sr genes identifying a single avirulence effector. A total of 24 unique effector gene candidates were identified, and haplotype analysis suggests that within this population, AvrSr5, AvrSr21, AvrSr8a, AvrSr17, and AvrSr9a are dominant avirulence genes, while avrSr9d is a dominant virulence gene. The putative effector genes will be fundamental for future effector gene cloning efforts, allowing for further understanding of rust effector biology and the mechanisms underlying virulence evolution in Pgt with respect to race-specific R-genes. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Arjun Upadhaya
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, U.S.A
| | - Sudha G C Upadhaya
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, U.S.A
| | - Robert Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, U.S.A
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22
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Guzman C, Mohri K, Nakamura R, Miyake M, Tsuchiya Y, Tomii K, Watanabe H. Neuronal and non-neuronal functions of the synaptic cell adhesion molecule neurexin in Nematostella vectensis. Nat Commun 2024; 15:6495. [PMID: 39090098 PMCID: PMC11294457 DOI: 10.1038/s41467-024-50818-8] [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: 03/20/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
The evolutionary transition from diffusion-mediated cell-cell communication to faster, targeted synaptic signaling in animal nervous systems is still unclear. Genome sequencing analyses have revealed a widespread distribution of synapse-related genes among early-diverging metazoans, but how synaptic machinery evolved remains largely unknown. Here, we examine the function of neurexins (Nrxns), a family of presynaptic cell adhesion molecules with critical roles in bilaterian chemical synapses, using the cnidarian model, Nematostella vectensis. Delta-Nrxns are expressed mainly in neuronal cell clusters that exhibit both peptidergic and classical neurotransmitter signaling. Knockdown of δ-Nrxn reduces spontaneous peristalsis of N. vectensis polyps. Interestingly, gene knockdown and pharmacological studies suggest that δ-Nrxn is involved in glutamate- and glycine-mediated signaling rather than peptidergic signaling. Knockdown of the epithelial α-Nrxn reveals a major role in cell adhesion between ectodermal and endodermal epithelia. Overall, this study provides molecular, functional, and cellular insights into the pre-neural function of Nrxns, as well as key information for understanding how and why they were recruited to the synaptic machinery.
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Affiliation(s)
- Christine Guzman
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Department of Biology, Institute of Zoology, University of Fribourg, CH-1700, Fribourg, Switzerland
| | - Kurato Mohri
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Ryotaro Nakamura
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Minato Miyake
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yuko Tsuchiya
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Kentaro Tomii
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Hiroshi Watanabe
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
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23
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McWhite CD, Sae-Lee W, Yuan Y, Mallam AL, Gort-Freitas NA, Ramundo S, Onishi M, Marcotte EM. Alternative proteoforms and proteoform-dependent assemblies in humans and plants. Mol Syst Biol 2024; 20:933-951. [PMID: 38918600 PMCID: PMC11297038 DOI: 10.1038/s44320-024-00048-3] [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: 02/01/2023] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
Abstract
The variability of proteins at the sequence level creates an enormous potential for proteome complexity. Exploring the depths and limits of this complexity is an ongoing goal in biology. Here, we systematically survey human and plant high-throughput bottom-up native proteomics data for protein truncation variants, where substantial regions of the full-length protein are missing from an observed protein product. In humans, Arabidopsis, and the green alga Chlamydomonas, approximately one percent of observed proteins show a short form, which we can assign by comparison to RNA isoforms as either likely deriving from transcript-directed processes or limited proteolysis. While some detected protein fragments align with known splice forms and protein cleavage events, multiple examples are previously undescribed, such as our observation of fibrocystin proteolysis and nuclear translocation in a green alga. We find that truncations occur almost entirely between structured protein domains, even when short forms are derived from transcript variants. Intriguingly, multiple endogenous protein truncations of phase-separating translational proteins resemble cleaved proteoforms produced by enteroviruses during infection. Some truncated proteins are also observed in both humans and plants, suggesting that they date to the last eukaryotic common ancestor. Finally, we describe novel proteoform-specific protein complexes, where the loss of a domain may accompany complex formation.
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Affiliation(s)
- Claire D McWhite
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
| | - Wisath Sae-Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Yaning Yuan
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Anna L Mallam
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | | | - Silvia Ramundo
- Gregor Mendel Institute of Molecular Plant Biology, 1030, Wien, Austria
| | - Masayuki Onishi
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
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24
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Vakirlis N, Kupczok A. Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins. Genome Res 2024; 34:888-903. [PMID: 38977308 PMCID: PMC11293555 DOI: 10.1101/gr.278977.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 06/12/2024] [Indexed: 07/10/2024]
Abstract
Species-specific genes, also known as orphans, are ubiquitous across life's domains. In prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in external elements such as viruses followed by horizontal gene transfer, whereas the scenario of native origination, through rapid divergence or de novo, is mostly dismissed. However, quantitative evidence supporting either scenario is lacking. Here, we systematically analyzed genomes from 4644 human gut microbiome species and identified more than 600,000 unique SSOGs, representing an average of 2.6% of a given species' pangenome. These sequences are mostly rare within each species yet show signs of purifying selection. Overall, SSOGs use optimal codons less frequently, and their proteins are more disordered than those of conserved genes (i.e., non-SSOGs). Importantly, across species, the GC content of SSOGs closely matches that of conserved ones. In contrast, the ∼5% of SSOGs that share similarity to known viral sequences have distinct characteristics, including lower GC content. Thus, SSOGs with similarity to viruses differ from the remaining SSOGs, contrasting an external origination scenario for most of them. By examining the orthologous genomic region in closely related species, we show that a small subset of SSOGs likely evolved natively de novo and find that these genes also differ in their properties from the remaining SSOGs. Our results challenge the notion that external elements are the dominant source of prokaryotic genetic novelty and will enable future studies into the biological role and relevance of species-specific genes in the human gut.
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Affiliation(s)
- Nikolaos Vakirlis
- Institute For Fundamental Biomedical Research, B.S.R.C. "Alexander Fleming," Vari 166 72, Greece;
- Institute for General Microbiology, Kiel University, 24118 Kiel, Germany
| | - Anne Kupczok
- Bioinformatics Group, Wageningen University, 6700 PB Wageningen, The Netherlands
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25
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Berasategui A, Salem H, Moller AG, Christopher Y, Vidaurre Montoya Q, Conn C, Read TD, Rodrigues A, Ziemert N, Gerardo N. Genomic insights into the evolution of secondary metabolism of Escovopsis and its allies, specialized fungal symbionts of fungus-farming ants. mSystems 2024; 9:e0057624. [PMID: 38904377 PMCID: PMC11265373 DOI: 10.1128/msystems.00576-24] [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: 04/24/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024] Open
Abstract
The metabolic intimacy of symbiosis often demands the work of specialists. Natural products and defensive secondary metabolites can drive specificity by ensuring infection and propagation across host generations. But in contrast to bacteria, little is known about the diversity and distribution of natural product biosynthetic pathways among fungi and how they evolve to facilitate symbiosis and adaptation to their host environment. In this study, we define the secondary metabolism of Escovopsis and closely related genera, symbionts in the gardens of fungus-farming ants. We ask how the gain and loss of various biosynthetic pathways correspond to divergent lifestyles. Long-read sequencing allowed us to define the chromosomal features of representative Escovopsis strains, revealing highly reduced genomes composed of seven to eight chromosomes. The genomes are highly syntenic with macrosynteny decreasing with increasing phylogenetic distance, while maintaining a high degree of mesosynteny. An ancestral state reconstruction analysis of biosynthetic pathways revealed that, while many secondary metabolites are shared with non-ant-associated Sordariomycetes, 56 pathways are unique to the symbiotic genera. Reflecting adaptation to diverging ant agricultural systems, we observe that the stepwise acquisition of these pathways mirrors the ecological radiations of attine ants and the dynamic recruitment and replacement of their fungal cultivars. As different clades encode characteristic combinations of biosynthetic gene clusters, these delineating profiles provide important insights into the possible mechanisms underlying specificity between these symbionts and their fungal hosts. Collectively, our findings shed light on the evolutionary dynamic nature of secondary metabolism in Escovopsis and its allies, reflecting adaptation of the symbionts to an ancient agricultural system.IMPORTANCEMicrobial symbionts interact with their hosts and competitors through a remarkable array of secondary metabolites and natural products. Here, we highlight the highly streamlined genomic features of attine-associated fungal symbionts. The genomes of Escovopsis species, as well as species from other symbiont genera, many of which are common with the gardens of fungus-growing ants, are defined by seven chromosomes. Despite a high degree of metabolic conservation, we observe some variation in the symbionts' potential to produce secondary metabolites. As the phylogenetic distribution of the encoding biosynthetic gene clusters coincides with attine transitions in agricultural systems, we highlight the likely role of these metabolites in mediating adaptation by a group of highly specialized symbionts.
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Affiliation(s)
- Aileen Berasategui
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Cluster of Excellence-Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen, Germany
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Hassan Salem
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen, Germany
| | - Abraham G. Moller
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yuliana Christopher
- Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Ciudad del Saber, Panamá City, Panama
| | - Quimi Vidaurre Montoya
- Department of General and Applied Biology, São Paulo State University (UNESP), Institute of Biosciences, Rio Claro, São Paulo, Brazil
| | - Caitlin Conn
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Department of Biology, Berry College, Mount Berry, Georgia, USA
| | - Timothy D. Read
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Andre Rodrigues
- Department of General and Applied Biology, São Paulo State University (UNESP), Institute of Biosciences, Rio Claro, São Paulo, Brazil
| | - Nadine Ziemert
- Cluster of Excellence-Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Nicole Gerardo
- Department of Biology, Emory University, Atlanta, Georgia, USA
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26
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Mpeyako LA, Hart AJ, Bailey NP, Carlton JM, Henrissat B, Sullivan SA, Hirt RP. Comparative genomics between Trichomonas tenax and Trichomonas vaginalis: CAZymes and candidate virulence factors. Front Microbiol 2024; 15:1437572. [PMID: 39086644 PMCID: PMC11288935 DOI: 10.3389/fmicb.2024.1437572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 06/28/2024] [Indexed: 08/02/2024] Open
Abstract
Introduction The oral trichomonad Trichomonas tenax is increasingly appreciated as a likely contributor to periodontitis, a chronic inflammatory disease induced by dysbiotic microbiota, in humans and domestic animals and is strongly associated with its worst prognosis. Our current understanding of the molecular basis of T. tenax interactions with host cells and the microbiota of the oral cavity are still rather limited. One laboratory strain of T. tenax (Hs-4:NIH/ATCC 30207) can be grown axenically and two draft genome assemblies have been published for that strain, although the structural and functional annotation of these genomes is not available. Methods GenSAS and Galaxy were used to annotate two publicly available draft genomes for T. tenax, with a focus on protein-coding genes. A custom pipeline was used to annotate the CAZymes for T. tenax and the human sexually transmitted parasite Trichomonas vaginalis, the most well-characterized trichomonad. A combination of bioinformatics analyses was used to screen for homologs of T. vaginalis virulence and colonization factors within the T. tenax annotated proteins. Results Our annotation of the two T. tenax draft genome sequences and their comparison with T. vaginalis proteins provide evidence for several candidate virulence factors. These include candidate surface proteins, secreted proteins and enzymes mediating potential interactions with host cells and/or members of the oral microbiota. The CAZymes annotation identified a broad range of glycoside hydrolase (GH) families, with the majority of these being shared between the two Trichomonas species. Discussion The presence of candidate T. tenax virulence genes supports the hypothesis that this species is associated with periodontitis through direct and indirect mechanisms. Notably, several GH proteins could represent potential new virulence factors for both Trichomonas species. These data support a model where T. tenax interactions with host cells and members of the oral microbiota could synergistically contribute to the damaging inflammation characteristic of periodontitis, supporting a causal link between T. tenax and periodontitis.
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Affiliation(s)
- Lenshina A. Mpeyako
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Adam J. Hart
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Nicholas P. Bailey
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jane M. Carlton
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, United States
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Lyngby, Denmark
| | - Steven A. Sullivan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, United States
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Robert P. Hirt
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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27
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Windels A, Franceus J, Pleiss J, Desmet T. CANDy: Automated analysis of domain architectures in carbohydrate-active enzymes. PLoS One 2024; 19:e0306410. [PMID: 38990885 PMCID: PMC11238990 DOI: 10.1371/journal.pone.0306410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/17/2024] [Indexed: 07/13/2024] Open
Abstract
Carbohydrate-active enzymes (CAZymes) can be found in all domains of life and play a crucial role in metabolic and physiological processes. CAZymes often possess a modular structure, comprising not only catalytic domains but also associated domains such as carbohydrate-binding modules (CBMs) and linker domains. By exploring the modular diversity of CAZy families, catalysts with novel properties can be discovered and further insight in their biological functions and evolutionary relationships can be obtained. Here we present the carbohydrate-active enzyme domain analysis tool (CANDy), an assembly of several novel scripts, tools and databases that allows users to analyze the domain architecture of all protein sequences in a given CAZy family. CANDy's usability is shown on glycoside hydrolase family 48, a small yet underexplored family containing multi-domain enzymes. Our analysis reveals the existence of 35 distinct domain assemblies, including eight known architectures, with the remaining assemblies awaiting characterization. Moreover, we substantiate the occurrence of horizontal gene transfer from prokaryotes to insect orthologs and provide evidence for the subsequent removal of auxiliary domains, likely through a gene fission event. CANDy is available at https://github.com/PyEED/CANDy.
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Affiliation(s)
- Alex Windels
- Department of Biotechnology, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
| | - Jorick Franceus
- Department of Biotechnology, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Tom Desmet
- Department of Biotechnology, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
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28
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Wan CY, Davis J, Chauhan M, Gleeson J, Prawer YJ, De Paoli-Iseppi R, Wells C, Choi J, Clark M. IsoVis - a webserver for visualization and annotation of alternative RNA isoforms. Nucleic Acids Res 2024; 52:W341-W347. [PMID: 38709877 PMCID: PMC11223830 DOI: 10.1093/nar/gkae343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/28/2024] [Accepted: 04/18/2024] [Indexed: 05/08/2024] Open
Abstract
Genes commonly express multiple RNA products (RNA isoforms), which differ in exonic content and can have different functions. Making sense of the plethora of known and novel RNA isoforms being identified by transcriptomic approaches requires a user-friendly way to visualize gene isoforms and how they differ in exonic content, expression levels and potential functions. Here we introduce IsoVis, a freely available webserver that accepts user-supplied transcriptomic data and visualizes the expressed isoforms in a clear, intuitive manner. IsoVis contains numerous features, including the ability to visualize all RNA isoforms of a gene and their expression levels; the annotation of known isoforms from external databases; mapping of protein domains and features to exons, allowing changes to protein sequence and function between isoforms to be established; and extensive species compatibility. Datasets visualised on IsoVis remain private to the user, allowing analysis of sensitive data. IsoVis visualisations can be downloaded to create publication-ready figures. The IsoVis webserver enables researchers to perform isoform analyses without requiring programming skills, is free to use, and available at https://isomix.org/isovis/.
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Affiliation(s)
- Ching Yin Wan
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Jack Davis
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Manveer Chauhan
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Josie Gleeson
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Yair D J Prawer
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Ricardo De Paoli-Iseppi
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Christine A Wells
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Jarny Choi
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Michael B Clark
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
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29
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Kuo CY, Tay RJ, Lin HC, Juan SC, Vidal-Diez de Ulzurrun G, Chang YC, Hoki J, Schroeder FC, Hsueh YP. The nematode-trapping fungus Arthrobotrys oligospora detects prey pheromones via G protein-coupled receptors. Nat Microbiol 2024; 9:1738-1751. [PMID: 38649409 DOI: 10.1038/s41564-024-01679-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
Abstract
The ability to sense prey-derived cues is essential for predatory lifestyles. Under low-nutrient conditions, Arthrobotrys oligospora and other nematode-trapping fungi develop dedicated structures for nematode capture when exposed to nematode-derived cues, including a conserved family of pheromones, the ascarosides. A. oligospora senses ascarosides via conserved MAPK and cAMP-PKA pathways; however, the upstream receptors remain unknown. Here, using genomic, transcriptomic and functional analyses, we identified two families of G protein-coupled receptors (GPCRs) involved in sensing distinct nematode-derived cues. GPCRs homologous to yeast glucose receptors are required for ascaroside sensing, whereas Pth11-like GPCRs contribute to ascaroside-independent nematode sensing. Both GPCR classes activate conserved cAMP-PKA signalling to trigger trap development. This work demonstrates that predatory fungi use multiple GPCRs to sense several distinct nematode-derived cues for prey recognition and to enable a switch to a predatory lifestyle. Identification of these receptors reveals the molecular mechanisms of cross-kingdom communication via conserved pheromones also sensed by plants and animals.
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Affiliation(s)
- Chih-Yen Kuo
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Rebecca J Tay
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Hung-Che Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Sheng-Chian Juan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | | | - Yu-Chu Chang
- Department of Biochemistry and Molecular Cell Biology, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jason Hoki
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Frank C Schroeder
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Yen-Ping Hsueh
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan.
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
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30
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Jiménez J, Mishra R, Wang X, Magee CM, Bonning BC. Composition and abundance of midgut plasma membrane proteins in two major hemipteran vectors of plant viruses, Bemisia tabaci and Myzus persicae. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 116:e22133. [PMID: 39054788 DOI: 10.1002/arch.22133] [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: 04/25/2024] [Revised: 06/13/2024] [Accepted: 06/29/2024] [Indexed: 07/27/2024]
Abstract
Multiple species within the order Hemiptera cause severe agricultural losses on a global scale. Aphids and whiteflies are of particular importance due to their role as vectors for hundreds of plant viruses, many of which enter the insect via the gut. To facilitate the identification of novel targets for disruption of plant virus transmission, we compared the relative abundance and composition of the gut plasma membrane proteomes of adult Bemisia tabaci (Hemiptera: Aleyrodidae) and Myzus persicae (Hemiptera: Aphididae), representing the first study comparing the gut plasma membrane proteomes of two different insect species. Brush border membrane vesicles were prepared from dissected guts, and proteins extracted, identified and quantified from triplicate samples via timsTOF mass spectrometry. A total of 1699 B. tabaci and 1175 M. persicae proteins were identified. Following bioinformatics analysis and manual curation, 151 B. tabaci and 115 M. persicae proteins were predicted to localize to the plasma membrane of the gut microvilli. These proteins were further categorized based on molecular function and biological process according to Gene Ontology terms. The most abundant gut plasma membrane proteins were identified. The ten plasma membrane proteins that differed in abundance between the two insect species were associated with the terms "protein binding" and "viral processes." In addition to providing insight into the gut physiology of hemipteran insects, these gut plasma membrane proteomes provide context for appropriate identification of plant virus receptors based on a combination of bioinformatic prediction and protein localization on the surface of the insect gut.
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Affiliation(s)
- Jaime Jiménez
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Ruchir Mishra
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Xinyue Wang
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Ciara M Magee
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Bryony C Bonning
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
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Lankford KP, Hulleman JD. Protocol for HiBiT tagging endogenous proteins using CRISPR-Cas9 gene editing. STAR Protoc 2024; 5:103000. [PMID: 38598333 PMCID: PMC11022101 DOI: 10.1016/j.xpro.2024.103000] [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: 01/03/2024] [Revised: 02/05/2024] [Accepted: 03/20/2024] [Indexed: 04/12/2024] Open
Abstract
We present a method of in vitro/in vivo protein detection by pairing CRISPR-Cas9 genome editing with the NanoBiT system. We describe steps for cell culturing, in vitro CRISPR-Cas9 ribonucleoprotein delivery, cell monitoring, efficiency assessments, and edit analysis through HiBiT assays. We then detail procedures to determine edit specificity through genomic DNA analysis, small interfering RNA reverse transfection, and HiBiT blotting. This protocol is simple to execute and multifunctional, and it enables high-throughput screens on endogenous proteins to be conducted with ease.
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Affiliation(s)
- Kaylee P Lankford
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - John D Hulleman
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, 2001 6(th) St. SE, Minneapolis, MN 55455, USA.
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Ravi J, Anantharaman V, Chen SZ, Brenner EP, Datta P, Aravind L, Gennaro ML. The phage shock protein (PSP) envelope stress response: discovery of novel partners and evolutionary history. mSystems 2024; 9:e0084723. [PMID: 38809013 PMCID: PMC11237479 DOI: 10.1128/msystems.00847-23] [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: 08/28/2023] [Accepted: 03/20/2024] [Indexed: 05/30/2024] Open
Abstract
Bacterial phage shock protein (PSP) systems stabilize the bacterial cell membrane and protect against envelope stress. These systems have been associated with virulence, but despite their critical roles, PSP components are not well characterized outside proteobacteria. Using comparative genomics and protein sequence-structure-function analyses, we systematically identified and analyzed PSP homologs, phyletic patterns, domain architectures, and gene neighborhoods. This approach underscored the evolutionary significance of the system, revealing that its core protein PspA (Snf7 in ESCRT outside bacteria) was present in the last universal common ancestor and that this ancestral functionality has since diversified into multiple novel, distinct PSP systems across life. Several novel partners of the PSP system were identified: (i) the Toastrack domain, likely facilitating assembly of sub-membrane stress-sensing and signaling complexes, (ii) the newly defined HTH-associated α-helical signaling domain-PadR-like transcriptional regulator pair system, and (iii) multiple independent associations with ATPase, CesT/Tir-like chaperone, and Band-7 domains in proteins thought to mediate sub-membrane dynamics. Our work also uncovered links between the PSP components and other domains, such as novel variants of SHOCT-like domains, suggesting roles in assembling membrane-associated complexes of proteins with disparate biochemical functions. Results are available at our interactive web app, https://jravilab.org/psp.IMPORTANCEPhage shock proteins (PSP) are virulence-associated, cell membrane stress-protective systems. They have mostly been characterized in Proteobacteria and Firmicutes. We now show that a minimal PSP system was present in the last universal common ancestor that evolved and diversified into newly identified functional contexts. Recognizing the conservation and evolution of PSP systems across bacterial phyla contributes to our understanding of stress response mechanisms in prokaryotes. Moreover, the newly discovered PSP modularity will likely prompt new studies of lineage-specific cell envelope structures, lifestyles, and adaptation mechanisms. Finally, our results validate the use of domain architecture and genetic context for discovery in comparative genomics.
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Affiliation(s)
- Janani Ravi
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
| | - Samuel Zorn Chen
- Computer Science Engineering Undergraduate Program, Michigan State University, East Lansing, Michigan, USA
| | - Evan Pierce Brenner
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Pratik Datta
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - L. Aravind
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
| | - Maria Laura Gennaro
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
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Ross PA, Xu W, Jalomo-Khayrova E, Bange G, Gumerov VM, Bradley PH, Sourjik V, Zhulin IB. Framework for exploring the sensory repertoire of the human gut microbiota. mBio 2024; 15:e0103924. [PMID: 38757952 PMCID: PMC11237719 DOI: 10.1128/mbio.01039-24] [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: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
Bacteria sense changes in their environment and transduce signals to adjust their cellular functions accordingly. For this purpose, bacteria employ various sensors feeding into multiple signal transduction pathways. Signal recognition by bacterial sensors is studied mainly in a few model organisms, but advances in genome sequencing and analysis offer new ways of exploring the sensory repertoire of many understudied organisms. The human gut is a natural target of this line of study: it is a nutrient-rich and dynamic environment and is home to thousands of bacterial species whose activities impact human health. Many gut commensals are also poorly studied compared to model organisms and are mainly known through their genome sequences. To begin exploring the signals human gut commensals sense and respond to, we have designed a framework that enables the identification of sensory domains, prediction of signals that they recognize, and experimental verification of these predictions. We validate this framework's functionality by systematically identifying amino acid sensors in selected bacterial genomes and metagenomes, characterizing their amino acid binding properties, and demonstrating their signal transduction potential.IMPORTANCESignal transduction is a central process governing how bacteria sense and respond to their environment. The human gut is a complex environment with many living organisms and fluctuating streams of nutrients. One gut inhabitant, Escherichia coli, is a model organism for studying signal transduction. However, E. coli is not representative of most gut microbes, and signaling pathways in the thousands of other organisms comprising the human gut microbiota remain poorly understood. This work provides a foundation for how to explore signals recognized by these organisms.
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Affiliation(s)
- Patricia A. Ross
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
| | - Wenhao Xu
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ekaterina Jalomo-Khayrova
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Vadim M. Gumerov
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
| | - Patrick H. Bradley
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Igor B. Zhulin
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
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Loveridge KM, Sigala PA. Identification of a divalent metal transporter required for cellular iron metabolism in malaria parasites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.587216. [PMID: 38798484 PMCID: PMC11118319 DOI: 10.1101/2024.05.10.587216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Plasmodium falciparum malaria parasites invade and multiply inside red blood cells (RBCs), the most iron-rich compartment in humans. Like all cells, P. falciparum requires nutritional iron to support essential metabolic pathways, but the critical mechanisms of iron acquisition and trafficking during RBC infection have remained obscure. Parasites internalize and liberate massive amounts of heme during large-scale digestion of RBC hemoglobin within an acidic food vacuole (FV) but lack a heme oxygenase to release porphyrin-bound iron. Although most FV heme is sequestered into inert hemozoin crystals, prior studies indicate that trace heme escapes biomineralization and is susceptible to non-enzymatic degradation within the oxidizing FV environment to release labile iron. Parasites retain a homolog of divalent metal transporter 1 (DMT1), a known mammalian iron transporter, but its role in P. falciparum iron acquisition has not been tested. Our phylogenetic studies indicate that P. falciparum DMT1 (PfDMT1) retains conserved molecular features critical for metal transport. We localized this protein to the FV membrane and defined its orientation in an export-competent topology. Conditional knockdown of PfDMT1 expression is lethal to parasites, which display broad cellular defects in iron-dependent functions, including impaired apicoplast biogenesis and mitochondrial polarization. Parasites are selectively rescued from partial PfDMT1 knockdown by supplementation with exogenous iron, but not other metals. These results support a cellular paradigm whereby PfDMT1 is the molecular gatekeeper to essential iron acquisition by blood-stage malaria parasites and suggest that therapeutic targeting of PfDMT1 may be a potent antimalarial strategy.
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Affiliation(s)
- Kade M. Loveridge
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Paul A. Sigala
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
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Aylward J, Wilson AM, Visagie CM, Spraker J, Barnes I, Buitendag C, Ceriani C, Del Mar Angel L, du Plessis D, Fuchs T, Gasser K, Krämer D, Li W, Munsamy K, Piso A, Price JL, Sonnekus B, Thomas C, van der Nest A, van Dijk A, van Heerden A, van Vuuren N, Yilmaz N, Duong TA, van der Merwe NA, Wingfield MJ, Wingfield BD. IMA Genome - F19 : A genome assembly and annotation guide to empower mycologists, including annotated draft genome sequences of Ceratocystis pirilliformis, Diaporthe australafricana, Fusarium ophioides, Paecilomyces lecythidis, and Sporothrix stenoceras. IMA Fungus 2024; 15:12. [PMID: 38831329 PMCID: PMC11149380 DOI: 10.1186/s43008-024-00142-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2024] [Indexed: 06/05/2024] Open
Abstract
The pace at which Next Generation Sequence data is being produced continues to accelerate as technology improves. As a result, such data are increasingly becoming accessible to biologists outside of the field of bioinformatics. In contrast, access to training in the methods of genome assembly and annotation are not growing at a similar rate. In this issue, we report on a Genome Assembly Workshop for Mycologists that was held at the Forestry and Agricultural Biotechnology Institute (FABI) at the University of Pretoria, South Africa and make available the 12 draft genome sequences emanating from the event. With the aim of making the process of genome assembly and annotation more accessible to biologists, we provide a step-by-step guide to both genome assembly and annotation, intended to encourage and empower mycologists to use genome data in their research.
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Affiliation(s)
- Janneke Aylward
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Andi M Wilson
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Cobus M Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Joseph Spraker
- Hexagon Bio, 1490 O'Brien Dr, Menlo Park, CA, 94025, USA
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Carla Buitendag
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Callin Ceriani
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Lina Del Mar Angel
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Deanné du Plessis
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Taygen Fuchs
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Katharina Gasser
- Department of Crop Sciences, University of Natural Resources and Life Sciences (BOKU), Institute of Plant Protection, Konrad Lorenz-Strasse 24, Tulln an Der Donau, 3430, Vienna, Austria
| | - Daniella Krämer
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - WenWen Li
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Kiara Munsamy
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Anja Piso
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Jenna-Lee Price
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Byron Sonnekus
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Chanel Thomas
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Ariska van der Nest
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Alida van Dijk
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Alishia van Heerden
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Nicole van Vuuren
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Neriman Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Nicolaas A van der Merwe
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa.
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Duart G, Graña-Montes R, Pastor-Cantizano N, Mingarro I. Experimental and computational approaches for membrane protein insertion and topology determination. Methods 2024; 226:102-119. [PMID: 38604415 DOI: 10.1016/j.ymeth.2024.03.012] [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: 11/07/2023] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
Membrane proteins play pivotal roles in a wide array of cellular processes and constitute approximately a quarter of the protein-coding genes across all organisms. Despite their ubiquity and biological significance, our understanding of these proteins remains notably less comprehensive compared to their soluble counterparts. This disparity in knowledge can be attributed, in part, to the inherent challenges associated with employing specialized techniques for the investigation of membrane protein insertion and topology. This review will center on a discussion of molecular biology methodologies and computational prediction tools designed to elucidate the insertion and topology of helical membrane proteins.
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Affiliation(s)
- Gerard Duart
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Ricardo Graña-Montes
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Noelia Pastor-Cantizano
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Ismael Mingarro
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain.
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Barco RA, Merino N, Lam B, Budnik B, Kaplan M, Wu F, Amend JP, Nealson KH, Emerson D. Comparative proteomics of a versatile, marine, iron-oxidizing chemolithoautotroph. Environ Microbiol 2024; 26:e16632. [PMID: 38861374 DOI: 10.1111/1462-2920.16632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/20/2024] [Indexed: 06/13/2024]
Abstract
This study conducted a comparative proteomic analysis to identify potential genetic markers for the biological function of chemolithoautotrophic iron oxidation in the marine bacterium Ghiorsea bivora. To date, this is the only characterized species in the class Zetaproteobacteria that is not an obligate iron-oxidizer, providing a unique opportunity to investigate differential protein expression to identify key genes involved in iron-oxidation at circumneutral pH. Over 1000 proteins were identified under both iron- and hydrogen-oxidizing conditions, with differentially expressed proteins found in both treatments. Notably, a gene cluster upregulated during iron oxidation was identified. This cluster contains genes encoding for cytochromes that share sequence similarity with the known iron-oxidase, Cyc2. Interestingly, these cytochromes, conserved in both Bacteria and Archaea, do not exhibit the typical β-barrel structure of Cyc2. This cluster potentially encodes a biological nanowire-like transmembrane complex containing multiple redox proteins spanning the inner membrane, periplasm, outer membrane, and extracellular space. The upregulation of key genes associated with this complex during iron-oxidizing conditions was confirmed by quantitative reverse transcription-PCR. These findings were further supported by electromicrobiological methods, which demonstrated negative current production by G. bivora in a three-electrode system poised at a cathodic potential. This research provides significant insights into the biological function of chemolithoautotrophic iron oxidation.
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Affiliation(s)
- Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - N Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Lawrence Livermore National Lab, Biosciences and Biotechnology Division, Livermore, California, USA
| | - B Lam
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - B Budnik
- Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts, USA
| | - M Kaplan
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - F Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, Zhejiang, China
| | - J P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - K H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - D Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
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Jamra G, Ghosh S, Singh N, Tripathy MK, Aggarwal A, Singh RDR, Srivastava AK, Kumar A, Pandey GK. Ectopic overexpression of Eleusine coracana CAX3 confers tolerance to metal and ion stress in yeast and Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108613. [PMID: 38696868 DOI: 10.1016/j.plaphy.2024.108613] [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: 09/12/2023] [Revised: 01/22/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024]
Abstract
Ionic and metal toxicity in plants is still a global problem for the environment, agricultural productivity and ultimately poses human health threats when these metal ions accumulate in edible organs of plants. Metal and ion transport from cytosol to the vacuole is considered an important component of metal and ion tolerance and a plant's potential utility in phytoremediation. Finger millet (Eleusine coracana) is an orphan crop but has prominent nutritional value in comparison to other cereals. Previous transcriptomic studies suggested that one of the calcium/proton exchanger (EcCAX3) is strongly upregulated during different developmental stages of spikes development in plant. This finding led us to speculate that high calcium accumulation in the grain might be because of CAX3 function. Moreover, phylogenetic analysis shows that EcCAX3 is more closely related to foxtail millet, sorghum and rice CAX3 protein. To decipher the functional role of EcCAX3, we have adopted complementation of yeast triple mutant K677 (Δpmc1Δvcx1Δcnb1), which has defective calcium transport machinery. Furthermore, metal tolerance assay shows that EcCAX3 expression conferred tolerance to different metal stresses in yeast. The gain-of-function study suggests that EcCAX3 overexpressing Arabidopsis plants shows better tolerance to higher concentration of different metal ions as compared to wild type Col-0 plants. EcCAX3-overexpression transgenic lines exhibits abundance of metal transporters and cation exchanger transporter transcripts under metal stress conditions. Furthermore, EcCAX3-overexpression lines have higher accumulation of macro- and micro-elements under different metal stress. Overall, this finding highlights the functional role of EcCAX3 in the regulation of metal and ion homeostasis and this could be potentially utilized to engineer metal fortification and generation of stress tolerant crops in near future.
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Affiliation(s)
- Gautam Jamra
- Dept. of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India; Dept. of Molecular Biology and Genetic Engineering, GBPUAT, Pantnagar Uttarakhand, 263145, India
| | - Soma Ghosh
- Dept. of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Nidhi Singh
- Dept. of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Manas Kumar Tripathy
- Dept. of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Aparna Aggarwal
- Dept. of Molecular Biology and Genetic Engineering, GBPUAT, Pantnagar Uttarakhand, 263145, India
| | - Reema Devi Rajan Singh
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Anil Kumar
- Dept. of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India; Dept. of Molecular Biology and Genetic Engineering, GBPUAT, Pantnagar Uttarakhand, 263145, India; Director Education, Rani Lakshmi Bai Central Agriculture University, Jhansi, NH-75, Near Pahuj Dam, Gwalior Road, Jhansi, Uttar Pradesh, 284003, India.
| | - Girdhar K Pandey
- Dept. of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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Aktaş E, Özdemir Özgentürk N. A comprehensive examination of ACE2 receptor and prediction of spike glycoprotein and ACE2 interaction based on in silico analysis of ACE2 receptor. J Biomol Struct Dyn 2024; 42:4412-4428. [PMID: 37349943 DOI: 10.1080/07391102.2023.2220814] [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: 02/12/2023] [Accepted: 05/28/2023] [Indexed: 06/24/2023]
Abstract
The ACE2 receptor plays a vital role not only in the SARS-CoV-induced epidemic but also in various other diseases, including cardiovascular diseases and ARDS. While studies have explored the interactions between ACE2 and SARS-CoV proteins, comprehensive research utilizing bioinformatic tools on the ACE2 protein has been lacking. The one aim of present study was to extensively analyze the regions of the ACE2 protein. After utilizing all bioinformatics tools especially G104 and L108 regions on ACE2 were come forward. The results of our analysis revealed that possible mutations or deletions in the G104 and L108 regions play a critical role in both the biological functioning and the determination of the chemical-physical properties of ACE2. Additionally, these regions were found to be more susceptible to mutations or deletions compared to other regions of the ACE2 protein. Notably, the randomly selected peptide, LQQNGSSVLS (100-109), which includes G104 and L108, exhibited a crucial role in binding the RBD of the spike protein, as supported by docking scores. Furthermore, both MDs and iMODs results provided evidence that G104 and L108 influence the dynamics of ACE2-spike complexes. This study is expected to offer a new perspective on the ACE2-SARS-CoV interaction and other research areas where ACE2 plays a significant role, such as biotechnology (protein engineering, enzyme optimization), medicine (RAS, pulmonary and cardiac diseases), and basic research (structural motifs, stabilizing protein folds, or facilitating important inter molecular contacts, protein's proper structure and function).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Emre Aktaş
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
| | - Nehir Özdemir Özgentürk
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
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40
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Deepika, Madhu, Upadhyay SK. Deciphering the features and functions of serine/arginine protein kinases in bread wheat. PLANT GENE 2024; 38:100451. [DOI: 10.1016/j.plgene.2024.100451] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/09/2024]
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Aguadé-Gorgorió J, Jami-Alahmadi Y, Calvanese V, Kardouh M, Fares I, Johnson H, Rezek V, Ma F, Magnusson M, Wang Y, Shin JE, Nance KJ, Goodridge HS, Liebscher S, Schenke-Layland K, Crooks GM, Wohlschlegel JA, Mikkola HKA. MYCT1 controls environmental sensing in human haematopoietic stem cells. Nature 2024; 630:412-420. [PMID: 38839950 PMCID: PMC11168926 DOI: 10.1038/s41586-024-07478-x] [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: 05/30/2023] [Accepted: 04/26/2024] [Indexed: 06/07/2024]
Abstract
The processes that govern human haematopoietic stem cell (HSC) self-renewal and engraftment are poorly understood and challenging to recapitulate in culture to reliably expand functional HSCs1-3. Here we identify MYC target 1 (MYCT1; also known as MTLC) as a crucial human HSC regulator that moderates endocytosis and environmental sensing in HSCs. MYCT1 is selectively expressed in undifferentiated human haematopoietic stem and progenitor cells (HSPCs) and endothelial cells but becomes markedly downregulated during HSC culture. Lentivirus-mediated knockdown of MYCT1 prevented human fetal liver and cord blood (CB) HSPC expansion and engraftment. By contrast, restoring MYCT1 expression improved the expansion and engraftment of cultured CB HSPCs. Single-cell RNA sequencing of human CB HSPCs in which MYCT1 was knocked down or overexpressed revealed that MYCT1 governs important regulatory programmes and cellular properties essential for HSC stemness, such as ETS factor expression and low mitochondrial activity. MYCT1 is localized in the endosomal membrane in HSPCs and interacts with vesicle trafficking regulators and signalling machinery. MYCT1 loss in HSPCs led to excessive endocytosis and hyperactive signalling responses, whereas restoring MYCT1 expression balanced culture-induced endocytosis and dysregulated signalling. Moreover, sorting cultured CB HSPCs on the basis of lowest endocytosis rate identified HSPCs with preserved MYCT1 expression and MYCT1-regulated HSC stemness programmes. Our work identifies MYCT1-moderated endocytosis and environmental sensing as essential regulatory mechanisms required to preserve human HSC stemness. Our data also pinpoint silencing of MYCT1 as a cell-culture-induced vulnerability that compromises human HSC expansion.
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Affiliation(s)
- Júlia Aguadé-Gorgorió
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA.
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA.
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
- Pfizer, Cambridge, MA, USA
| | - Vincenzo Calvanese
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA
- Laboratory for Molecular Cell Biology, University College London, London, UK
- Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Maya Kardouh
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- Oakland University William Beaumont School of Medicine, Rochester, MI, USA
| | - Iman Fares
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- Kite Pharma, Santa Monica, CA, USA
| | - Haley Johnson
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Valerie Rezek
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- UCLA AIDS Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Feiyang Ma
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA
- Amgen, Thousand Oaks, CA, USA
| | - Mattias Magnusson
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Yanling Wang
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Juliana E Shin
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Karina J Nance
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Helen S Goodridge
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Simone Liebscher
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Eberhard Karls University, Tübingen, Germany
| | - Katja Schenke-Layland
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Eberhard Karls University, Tübingen, Germany
- NMI Natural and Medical Sciences Institute at the University Tübingen, Reutlingen, Germany
| | - Gay M Crooks
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Hanna K A Mikkola
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA.
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA.
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Zhiganov NI, Vinokurov KS, Salimgareev RS, Tereshchenkova VF, Dunaevsky YE, Belozersky MA, Elpidina EN. The Set of Serine Peptidases of the Tenebrio molitor Beetle: Transcriptomic Analysis on Different Developmental Stages. Int J Mol Sci 2024; 25:5743. [PMID: 38891931 PMCID: PMC11172050 DOI: 10.3390/ijms25115743] [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: 04/16/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
Serine peptidases (SPs) of the chymotrypsin S1A subfamily are an extensive group of enzymes found in all animal organisms, including insects. Here, we provide analysis of SPs in the yellow mealworm Tenebrio molitor transcriptomes and genomes datasets and profile their expression patterns at various stages of ontogeny. A total of 269 SPs were identified, including 137 with conserved catalytic triad residues, while 125 others lacking conservation were proposed as non-active serine peptidase homologs (SPHs). Seven deduced sequences exhibit a complex domain organization with two or three peptidase units (domains), predicted both as active or non-active. The largest group of 84 SPs and 102 SPHs had no regulatory domains in the propeptide, and the majority of them were expressed only in the feeding life stages, larvae and adults, presumably playing an important role in digestion. The remaining 53 SPs and 23 SPHs had different regulatory domains, showed constitutive or upregulated expression at eggs or/and pupae stages, participating in regulation of various physiological processes. The majority of polypeptidases were mainly expressed at the pupal and adult stages. The data obtained expand our knowledge on SPs/SPHs and provide the basis for further studies of the functions of proteins from the S1A subfamily in T. molitor.
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Affiliation(s)
- Nikita I. Zhiganov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (N.I.Z.); (Y.E.D.); (M.A.B.)
| | - Konstantin S. Vinokurov
- Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budejovice, Czech Republic;
| | - Ruslan S. Salimgareev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia;
| | | | - Yakov E. Dunaevsky
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (N.I.Z.); (Y.E.D.); (M.A.B.)
| | - Mikhail A. Belozersky
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (N.I.Z.); (Y.E.D.); (M.A.B.)
| | - Elena N. Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (N.I.Z.); (Y.E.D.); (M.A.B.)
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Kok CR, Rose DJ, Cui J, Whisenhunt L, Hutkins R. Identification of carbohydrate gene clusters obtained from in vitro fermentations as predictive biomarkers of prebiotic responses. BMC Microbiol 2024; 24:183. [PMID: 38796418 PMCID: PMC11127362 DOI: 10.1186/s12866-024-03344-y] [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: 10/15/2023] [Accepted: 05/21/2024] [Indexed: 05/28/2024] Open
Abstract
BACKGROUND Prebiotic fibers are non-digestible substrates that modulate the gut microbiome by promoting expansion of microbes having the genetic and physiological potential to utilize those molecules. Although several prebiotic substrates have been consistently shown to provide health benefits in human clinical trials, responder and non-responder phenotypes are often reported. These observations had led to interest in identifying, a priori, prebiotic responders and non-responders as a basis for personalized nutrition. In this study, we conducted in vitro fecal enrichments and applied shotgun metagenomics and machine learning tools to identify microbial gene signatures from adult subjects that could be used to predict prebiotic responders and non-responders. RESULTS Using short chain fatty acids as a targeted response, we identified genetic features, consisting of carbohydrate active enzymes, transcription factors and sugar transporters, from metagenomic sequencing of in vitro fermentations for three prebiotic substrates: xylooligosacharides, fructooligosacharides, and inulin. A machine learning approach was then used to select substrate-specific gene signatures as predictive features. These features were found to be predictive for XOS responders with respect to SCFA production in an in vivo trial. CONCLUSIONS Our results confirm the bifidogenic effect of commonly used prebiotic substrates along with inter-individual microbial responses towards these substrates. We successfully trained classifiers for the prediction of prebiotic responders towards XOS and inulin with robust accuracy (≥ AUC 0.9) and demonstrated its utility in a human feeding trial. Overall, the findings from this study highlight the practical implementation of pre-intervention targeted profiling of individual microbiomes to stratify responders and non-responders.
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Affiliation(s)
- Car Reen Kok
- Complex Biosystems, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Devin J Rose
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Food Science and Technology, University of Nebraska, 268 Food Innovation Center, Lincoln, NE, 68588, USA
| | - Juan Cui
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Lisa Whisenhunt
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Robert Hutkins
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
- Department of Food Science and Technology, University of Nebraska, 268 Food Innovation Center, Lincoln, NE, 68588, USA.
- Department of Food Science and Technology, University of Nebraska, 258 Food Innovation Center, Lincoln, NE, 68588-6205, USA.
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Lam AHC, Cooke A, Wright H, Lawson DM, Charpentier M. Evolution of endosymbiosis-mediated nuclear calcium signaling in land plants. Curr Biol 2024; 34:2212-2220.e7. [PMID: 38642549 DOI: 10.1016/j.cub.2024.03.063] [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: 01/31/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/22/2024]
Abstract
The ability of fungi to establish mycorrhizal associations with plants and enhance the acquisition of mineral nutrients stands out as a key feature of terrestrial life. Evidence indicates that arbuscular mycorrhizal (AM) association is a trait present in the common ancestor of land plants,1,2,3,4 suggesting that AM symbiosis was an important adaptation for plants in terrestrial environments.5 The activation of nuclear calcium signaling in roots is essential for AM within flowering plants.6 Given that the earliest land plants lacked roots, whether nuclear calcium signals are required for AM in non-flowering plants is unknown. To address this question, we explored the functional conservation of symbiont-induced nuclear calcium signals between the liverwort Marchantia paleacea and the legume Medicago truncatula. In M. paleacea, AM fungi penetrate the rhizoids and form arbuscules in the thalli.7 Here, we demonstrate that AM germinating spore exudate (GSE) activates nuclear calcium signals in the rhizoids of M. paleacea and that this activation is dependent on the nuclear-localized ion channel DOES NOT MAKE INFECTIONS 1 (MpaDMI1). However, unlike flowering plants, MpaDMI1-mediated calcium signaling is only required for the thalli colonization but not for the AM penetration within rhizoids. We further demonstrate that the mechanism of regulation of DMI1 has diverged between M. paleacea and M. truncatula, including a key amino acid residue essential to sustain DMI1 in an inactive state. Our study reveals functional evolution of nuclear calcium signaling between liverworts and flowering plants and opens new avenues of research into the mechanism of endosymbiosis signaling.
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Affiliation(s)
- Anson H C Lam
- John Innes Centre, Cell and Developmental Biology Department, Norwich Research Park, Norwich NR4 7UH, UK
| | - Aisling Cooke
- John Innes Centre, Cell and Developmental Biology Department, Norwich Research Park, Norwich NR4 7UH, UK
| | - Hannah Wright
- John Innes Centre, Cell and Developmental Biology Department, Norwich Research Park, Norwich NR4 7UH, UK
| | - David M Lawson
- John Innes Centre, Biochemistry and Metabolism Department, Norwich Research Park, Norwich NR4 7UH, UK
| | - Myriam Charpentier
- John Innes Centre, Cell and Developmental Biology Department, Norwich Research Park, Norwich NR4 7UH, UK.
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Toth R, Ilic AM, Huettel B, Duduk B, Kube M. Divergence within the Taxon ' Candidatus Phytoplasma asteris' Confirmed by Comparative Genome Analysis of Carrot Strains. Microorganisms 2024; 12:1016. [PMID: 38792845 PMCID: PMC11123874 DOI: 10.3390/microorganisms12051016] [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: 03/19/2024] [Revised: 04/30/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Phytoplasmas are linked to diseases in hundreds of economically important crops, including carrots. In carrots, phytoplasmosis is associated with leaf chlorosis and necrosis, coupled with inhibited root system development, ultimately leading to significant economic losses. During a field study conducted in Baden-Württemberg (Germany), two strains of the provisional taxon 'Candidatus Phytoplasma asteris' were identified within a carrot plot. For further analysis, strains M8 and M33 underwent shotgun sequencing, utilising single-molecule-real-time (SMRT) long-read sequencing and sequencing-by-synthesis (SBS) paired-end short-read sequencing techniques. Hybrid assemblies resulted in complete de novo assemblies of two genomes harboring circular chromosomes and two plasmids. Analyses, including average nucleotide identity and sequence comparisons of established marker genes, confirmed the phylogenetic divergence of 'Ca. P. asteris' and a different assignment of strains to the 16S rRNA subgroup I-A for M33 and I-B for M8. These groups exhibited unique features, encompassing virulence factors and genes, associated with the mobilome. In contrast, pan-genome analysis revealed a highly conserved gene set related to metabolism across these strains. This analysis of the Aster Yellows (AY) group reaffirms the perception of phytoplasmas as bacteria that have undergone extensive genome reduction during their co-evolution with the host and an increase of genome size by mobilome.
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Affiliation(s)
- Rafael Toth
- Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, 70599 Stuttgart, Germany; (R.T.); (A.-M.I.)
| | - Anna-Marie Ilic
- Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, 70599 Stuttgart, Germany; (R.T.); (A.-M.I.)
| | | | - Bojan Duduk
- Institute of Pesticides and Environmental Protection, 11080 Belgrade, Serbia;
| | - Michael Kube
- Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, 70599 Stuttgart, Germany; (R.T.); (A.-M.I.)
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Charneau S, de Oliveira LS, Zenonos Z, Hopp CS, Bastos IMD, Loew D, Lombard B, Pandolfo Silveira A, de Carvalho Nardeli Basílio Lobo G, Bao SN, Grellier P, Rayner JC. APEX2-based proximity proteomic analysis identifies candidate interactors for Plasmodium falciparum knob-associated histidine-rich protein in infected erythrocytes. Sci Rep 2024; 14:11242. [PMID: 38755230 PMCID: PMC11099048 DOI: 10.1038/s41598-024-61295-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/03/2024] [Indexed: 05/18/2024] Open
Abstract
The interaction of Plasmodium falciparum-infected red blood cells (iRBCs) with the vascular endothelium plays a crucial role in malaria pathology and disease. KAHRP is an exported P. falciparum protein involved in iRBC remodelling, which is essential for the formation of protrusions or "knobs" on the iRBC surface. These knobs and the proteins that are concentrated within them allow the parasites to escape the immune response and host spleen clearance by mediating cytoadherence of the iRBC to the endothelial wall, but this also slows down blood circulation, leading in some cases to severe cerebral and placental complications. In this work, we have applied genetic and biochemical tools to identify proteins that interact with P. falciparum KAHRP using enhanced ascorbate peroxidase 2 (APEX2) proximity-dependent biotinylation and label-free shotgun proteomics. A total of 30 potential KAHRP-interacting candidates were identified, based on the assigned fragmented biotinylated ions. Several identified proteins have been previously reported to be part of the Maurer's clefts and knobs, where KAHRP resides. This study may contribute to a broader understanding of P. falciparum protein trafficking and knob architecture and shows for the first time the feasibility of using APEX2-proximity labelling in iRBCs.
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Affiliation(s)
- Sébastien Charneau
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil.
| | - Lucas Silva de Oliveira
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil
- UMR 7245 MCAM Molecules of Communication and Adaptation of Microorganisms, Muséum National d'Histoire Naturelle, CNRS, 75231, Paris Cedex 05, France
| | - Zenon Zenonos
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Biologics Engineering, Oncology R&D, AstraZenecaGranta Park, Cambridge, UK
| | - Christine S Hopp
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Izabela M D Bastos
- Laboratory of Host Pathogen Interaction, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil
| | - Damarys Loew
- Institut Curie, Centre de Recherche, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Bérangère Lombard
- Institut Curie, Centre de Recherche, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Ariane Pandolfo Silveira
- Laboratory of Microscopy and Microanalysis, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | | | - Sônia Nair Bao
- Laboratory of Microscopy and Microanalysis, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | - Philippe Grellier
- UMR 7245 MCAM Molecules of Communication and Adaptation of Microorganisms, Muséum National d'Histoire Naturelle, CNRS, 75231, Paris Cedex 05, France
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
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Thiel D, Yañez Guerra LA, Kieswetter A, Cole AG, Temmerman L, Technau U, Jékely G. Large-scale deorphanization of Nematostella vectensis neuropeptide G protein-coupled receptors supports the independent expansion of bilaterian and cnidarian peptidergic systems. eLife 2024; 12:RP90674. [PMID: 38727714 PMCID: PMC11087051 DOI: 10.7554/elife.90674] [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] [Indexed: 05/12/2024] Open
Abstract
Neuropeptides are ancient signaling molecules in animals but only few peptide receptors are known outside bilaterians. Cnidarians possess a large number of G protein-coupled receptors (GPCRs) - the most common receptors of bilaterian neuropeptides - but most of these remain orphan with no known ligands. We searched for neuropeptides in the sea anemone Nematostella vectensis and created a library of 64 peptides derived from 33 precursors. In a large-scale pharmacological screen with these peptides and 161 N. vectensis GPCRs, we identified 31 receptors specifically activated by 1 to 3 of 14 peptides. Mapping GPCR and neuropeptide expression to single-cell sequencing data revealed how cnidarian tissues are extensively connected by multilayer peptidergic networks. Phylogenetic analysis identified no direct orthology to bilaterian peptidergic systems and supports the independent expansion of neuropeptide signaling in cnidarians from a few ancestral peptide-receptor pairs.
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Affiliation(s)
- Daniel Thiel
- Living Systems Institute, University of ExeterExeterUnited Kingdom
| | | | - Amanda Kieswetter
- Animal Physiology & Neurobiology, Department of Biology, University of LeuvenLeuvenBelgium
| | - Alison G Cole
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of ViennaViennaAustria
| | - Liesbet Temmerman
- Animal Physiology & Neurobiology, Department of Biology, University of LeuvenLeuvenBelgium
| | - Ulrich Technau
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of ViennaViennaAustria
| | - Gáspár Jékely
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- Centre for Organismal Studies (COS), Heidelberg UniversityHeidelbergGermany
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Khan MM, Sidorczuk K, Becker J, Aleksandrowicz A, Baraniewicz K, Ludwig C, Ali A, Kingsley RA, Schierack P, Kolenda R. Characterization of clumpy adhesion of Escherichia coli to human cells and associated factors influencing antibiotic sensitivity. Microbiol Spectr 2024; 12:e0260623. [PMID: 38530058 PMCID: PMC11064533 DOI: 10.1128/spectrum.02606-23] [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: 06/24/2023] [Accepted: 03/12/2024] [Indexed: 03/27/2024] Open
Abstract
Escherichia coli intestinal infection pathotypes are characterized by distinct adhesion patterns, including the recently described clumpy adhesion phenotype. Here, we identify and characterize the genetic factors contributing to the clumpy adhesion of E. coli strain 4972. In this strain, the transcriptome and proteome of adhered bacteria were found to be distinct from planktonic bacteria in the supernatant. A total of 622 genes in the transcriptome were differentially expressed in bacteria present in clumps relative to the planktonic bacteria. Seven genes targeted for disruption had variable distribution in different pathotypes and nonpathogenic E. coli, with the pilV and spnT genes being the least frequent or absent from most groups. Deletion (Δ) of five differentially expressed genes, flgH, ffp, pilV, spnT, and yggT, affected motility, adhesion, or antibiotic stress. ΔflgH exhibited 80% decrease and ΔyggT depicted 184% increase in adhesion, and upon complementation, adhesion was significantly reduced to 13%. ΔflgH lost motility and was regenerated when complemented, whereas Δffp had significantly increased motility, and reintroduction of the same gene reduced it to the wild-type level. The clumps produced by Δffp and ΔspnT were more resistant and protected the bacteria, with ΔspnT showing the best clump formation in terms of ampicillin stress protection. ΔyggT had the lowest tolerance to gentamicin, where the antibiotic stress completely eliminated the bacteria. Overall, we were able to investigate the influence of clump formation on cell surface adhesion and antimicrobial tolerance, with the contribution of several factors crucial to clump formation on susceptibility to the selected antibiotics. IMPORTANCE The study explores a biofilm-like clumpy adhesion phenotype in Escherichia coli, along with various factors and implications for antibiotic susceptibility. The phenotype permitted the bacteria to survive the onslaught of high antibiotic concentrations. Profiles of the transcriptome and proteome allowed the differentiation between adhered bacteria in clumps and planktonic bacteria in the supernatant. The deletion mutants of genes differentially expressed between adhered and planktonic bacteria, i.e., flgH, ffp, pilV, spnT, and yggT, and respective complementations in trans cemented their roles in multiple capacities. ffp, an uncharacterized gene, is involved in motility and resistance to ampicillin in a clumpy state. The work also affirms for the first time the role of the yggT gene in adhesion and its involvement in susceptibility against another aminoglycoside antibiotic, i.e., gentamicin. Overall, the study contributes to the mechanisms of biofilm-like adhesion phenotype and understanding of the antimicrobial therapy failures and infections of E. coli.
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Affiliation(s)
- Muhammad Moman Khan
- Institute for Biotechnology, Brandenburg University of Technology (BTU) Cottbus-Senftenberg, Senftenberg, Germany
| | - Katarzyna Sidorczuk
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Juliane Becker
- Institute for Biotechnology, Brandenburg University of Technology (BTU) Cottbus-Senftenberg, Senftenberg, Germany
| | - Adrianna Aleksandrowicz
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Karolina Baraniewicz
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wrocław, Wrocław, Poland
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences, Technical University Munich (TUM), Munich, Germany
| | - Aamir Ali
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Robert A. Kingsley
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Peter Schierack
- Institute for Biotechnology, Brandenburg University of Technology (BTU) Cottbus-Senftenberg, Senftenberg, Germany
| | - Rafał Kolenda
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
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Andrade KCR, Homem-de-Mello M, Motta JA, Borges MG, de Abreu JAC, de Souza PM, Pessoa A, Pappas GJ, de Oliveira Magalhães P. A Structural In Silico Analysis of the Immunogenicity of L-Asparaginase from Penicillium cerradense. Int J Mol Sci 2024; 25:4788. [PMID: 38732010 PMCID: PMC11084778 DOI: 10.3390/ijms25094788] [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: 03/26/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
L-asparaginase is an essential drug used to treat acute lymphoid leukemia (ALL), a cancer of high prevalence in children. Several adverse reactions associated with L-asparaginase have been observed, mainly caused by immunogenicity and allergenicity. Some strategies have been adopted, such as searching for new microorganisms that produce the enzyme and applying protein engineering. Therefore, this work aimed to elucidate the molecular structure and predict the immunogenic profile of L-asparaginase from Penicillium cerradense, recently revealed as a new fungus of the genus Penicillium and producer of the enzyme, as a motivation to search for alternatives to bacterial L-asparaginase. In the evolutionary relationship, L-asparaginase from P. cerradense closely matches Aspergillus species. Using in silico tools, we characterized the enzyme as a protein fragment of 378 amino acids (39 kDa), including a signal peptide containing 17 amino acids, and the isoelectric point at 5.13. The oligomeric state was predicted to be a homotetramer. Also, this L-asparaginase presented a similar immunogenicity response (T- and B-cell epitopes) compared to Escherichia coli and Dickeya chrysanthemi enzymes. These results suggest a potentially useful L-asparaginase, with insights that can drive strategies to improve enzyme production.
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Affiliation(s)
- Kellen Cruvinel Rodrigues Andrade
- Laboratory of Natural Products, Department of Pharmacy, Faculty of Health Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (K.C.R.A.)
| | - Mauricio Homem-de-Mello
- inSiliTox, Department of Pharmacy, Faculty of Health Sciences, University of Brasilia, Brasilia 70910-900, Brazil
| | - Julia Almeida Motta
- inSiliTox, Department of Pharmacy, Faculty of Health Sciences, University of Brasilia, Brasilia 70910-900, Brazil
| | - Marina Guimarães Borges
- Laboratory of Natural Products, Department of Pharmacy, Faculty of Health Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (K.C.R.A.)
| | - Joel Antônio Cordeiro de Abreu
- Laboratory of Natural Products, Department of Pharmacy, Faculty of Health Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (K.C.R.A.)
| | - Paula Monteiro de Souza
- Laboratory of Natural Products, Department of Pharmacy, Faculty of Health Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (K.C.R.A.)
| | - Adalberto Pessoa
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Georgios J. Pappas
- Department Cell Biology, Institute Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil
| | - Pérola de Oliveira Magalhães
- Laboratory of Natural Products, Department of Pharmacy, Faculty of Health Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (K.C.R.A.)
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Castell-Miller CV, Kono TJ, Ranjan A, Schlatter DC, Samac DA, Kimball JA. Interactive transcriptome analyses of Northern Wild Rice ( Zizania palustris L.) and Bipolaris oryzae show convoluted communications during the early stages of fungal brown spot development. FRONTIERS IN PLANT SCIENCE 2024; 15:1350281. [PMID: 38736448 PMCID: PMC11086184 DOI: 10.3389/fpls.2024.1350281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/02/2024] [Indexed: 05/14/2024]
Abstract
Fungal diseases, caused mainly by Bipolaris spp., are past and current threats to Northern Wild Rice (NWR) grain production and germplasm preservation in both natural and cultivated settings. Genetic resistance against the pathogen is scarce. Toward expanding our understanding of the global gene communications of NWR and Bipolaris oryzae interaction, we designed an RNA sequencing study encompassing the first 12 h and 48 h of their encounter. NWR activated numerous plant recognition receptors after pathogen infection, followed by active transcriptional reprogramming of signaling mechanisms driven by Ca2+ and its sensors, mitogen-activated protein kinase cascades, activation of an oxidative burst, and phytohormone signaling-bound mechanisms. Several transcription factors associated with plant defense were found to be expressed. Importantly, evidence of diterpenoid phytoalexins, especially phytocassane biosynthesis, among expression of other defense genes was found. In B. oryzae, predicted genes associated with pathogenicity including secreted effectors that could target plant defense mechanisms were expressed. This study uncovered the early molecular communication between the NWR-B. oryzae pathosystem, which could guide selection for allele-specific genes to boost NWR defenses, and overall aid in the development of more efficient selection methods in NWR breeding through the use of the most virulent fungal isolates.
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Affiliation(s)
| | - Thomas J.Y. Kono
- Minnesota Supercomputing Institute, University of Minnesota, Saint Paul, MN, United States
| | - Ashish Ranjan
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Daniel C. Schlatter
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
- United States Department of Agriculture, Agricultural Research Service, Plant Science Research Unit, Saint Paul, MN, United States
| | - Deborah A. Samac
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
- United States Department of Agriculture, Agricultural Research Service, Plant Science Research Unit, Saint Paul, MN, United States
| | - Jennifer A. Kimball
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
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