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      Essential role of the conserved oligomeric Golgi complex in Toxoplasma gondii

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          ABSTRACT

          Survival of the apicomplexan parasite Toxoplasma gondii depends on the proper functioning of many glycosylated proteins. Glycosylation is performed in the major membranous organelles ER and Golgi apparatus that constitute a significant portion of the intracellular secretory system. The secretory pathway is bidirectional: cargo is delivered to target organelles in the anterograde direction, while retrograde flow maintains the membrane balance and proper localization of glycosylation machinery. Despite the vital role of the Golgi in parasite infectivity, little is known about its biogenesis in apicomplexan parasites. In this study, we examined the T. gondii conserved oligomeric Golgi (COG) complex and determined that contrary to predictions, T. gondii expresses the entire eight-subunit complex and that each complex subunit is essential for tachyzoite growth. Deprivation of the COG complex induces a pronounced effect on Golgi and ER membranes, which suggests that the T. gondii COG complex has a wider role in intracellular membrane trafficking. We demonstrated that besides its conservative role in retrograde intra-Golgi trafficking, the COG complex also interacted with anterograde and novel transport machinery. Furthermore, we identified coccidian-specific components of the Golgi transport system: TgUlp1 and TgGlp1. Protein structure and phylogenetic analyses revealed that TgUlp1 is an adaptation of the conservative Golgi tethering factor Uso1/p115. TgUlp1 and together with Golgi-localized TgGlp1 showed dominant interactions with the trafficking machinery that was predicted to operate endosome-to-Golgi recycling. Together, our study showed that T. gondii has expanded the function of the conservative Golgi tethering COG complex and evolved additional regulators of transport that are likely to serve parasite-specific secretory organelles.

          IMPORTANCE

          The Golgi is an essential eukaryotic organelle and a major place for protein sorting and glycosylation. Among apicomplexan parasites, Toxoplasma gondii retains the most developed Golgi structure and produces many glycosylated factors necessary for parasite survival. Despite its importance, Golgi function received little attention in the past. In the current study, we identified and characterized the conserved oligomeric Golgi complex and its novel partners critical for protein transport in T. gondii tachyzoites. Our results suggest that T. gondii broadened the role of the conserved elements and reinvented the missing components of the trafficking machinery to accommodate the specific needs of the opportunistic parasite T. gondii.

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          MUSCLE: multiple sequence alignment with high accuracy and high throughput.

          We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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            SWISS-MODEL: homology modelling of protein structures and complexes

            Abstract Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated workflows and servers simplify and streamline the homology modelling process, also allowing users without a specific computational expertise to generate reliable protein models and have easy access to modelling results, their visualization and interpretation. Here, we present an update to the SWISS-MODEL server, which pioneered the field of automated modelling 25 years ago and been continuously further developed. Recently, its functionality has been extended to the modelling of homo- and heteromeric complexes. Starting from the amino acid sequences of the interacting proteins, both the stoichiometry and the overall structure of the complex are inferred by homology modelling. Other major improvements include the implementation of a new modelling engine, ProMod3 and the introduction a new local model quality estimation method, QMEANDisCo. SWISS-MODEL is freely available at https://swissmodel.expasy.org.
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              New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

              PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
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                Author and article information

                Contributors
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: ValidationRole: VisualizationRole: Writing – original draft
                Role: Data curationRole: Formal analysisRole: MethodologyRole: ValidationRole: Writing – original draft
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: ValidationRole: Writing – original draft
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: ValidationRole: Writing – original draft
                Role: Data curationRole: Formal analysisRole: MethodologyRole: SoftwareRole: ValidationRole: Writing – original draft
                Role: Data curationRole: InvestigationRole: MethodologyRole: ResourcesRole: Writing – original draftRole: Writing – review and editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: Writing – original draftRole: Writing – review and editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review and editing
                Role: Editor
                Journal
                mBio
                mBio
                mbio
                mBio
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2150-7511
                Nov-Dec 2023
                15 November 2023
                15 November 2023
                : 14
                : 6
                : e02513-23
                Affiliations
                [1 ]Division of Infectious Diseases, Department of Internal Medicine, Morsani College of Medicine, University of South Florida; , Tampa, Florida, USA
                [2 ]Department of Physiology and Cell Biology, College of Medicine, University of Arkansas for Medical Sciences; , Little Rock, Arkansas, USA
                [3 ]College of Public Health, University of South Florida; , Tampa, Florida, USA
                [4 ]Proteomics Core, College of Arts and Sciences, University of South Florida; , Tampa, Florida, USA
                University of Pittsburgh; , Pittsburgh, Pennsylvania, USA
                Author notes
                Address correspondence to Elena S. Suvorova, suvorova@ 123456usf.edu

                Clem Marsilia and Mrinalini Batra contributed equally to this article. Author order was determined by drawing straws.

                The authors declare no conflict of interest.

                Author information
                https://orcid.org/0009-0007-1273-3665
                https://orcid.org/0009-0005-9520-6144
                https://orcid.org/0000-0003-4482-8144
                Article
                02513-23 mbio.02513-23
                10.1128/mbio.02513-23
                10746232
                37966241
                bbf77b38-f4d9-4c34-9560-c397e4673914
                Copyright © 2023 Marsilia et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 18 September 2023
                : 05 October 2023
                Page count
                supplementary-material: 9, authors: 8, Figures: 9, References: 83, Pages: 24, Words: 12498
                Funding
                Funded by: HHS | NIH | NIAID | Division of Intramural Research, National Institute of Allergy and Infectious Diseases (DIR, NIAID);
                Award ID: AI141467
                Award Recipient :
                Funded by: HHS | NIH | National Institute of General Medical Sciences (NIGMS);
                Award ID: GM083144
                Award Recipient :
                Categories
                Research Article
                parasitology, Parasitology
                Custom metadata
                November/December 2023

                Life sciences
                apicomplexa,toxoplasma gondii,golgi,vesicular transport,retrograde transport,anterograde transport,copi,copii,ap-5,glycosylation

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