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Full-Text Articles in Life Sciences
Ribosomal Protein L10 Is Encoded In The Mitochondrial Genome Of Many Land Plants And Green Algae, Jeffrey P. Mower, Linda Bonen
Ribosomal Protein L10 Is Encoded In The Mitochondrial Genome Of Many Land Plants And Green Algae, Jeffrey P. Mower, Linda Bonen
Center for Plant Science Innovation: Faculty and Staff Publications
Background: The mitochondrial genomes of plants generally encode 30-40 identified protein-coding genes and a large number of lineage-specific ORFs. The lack of wide conservation for most ORFs suggests they are unlikely to be functional. However, an ORF, termed orf-bryo1, was recently found to be conserved among bryophytes suggesting that it might indeed encode a functional mitochondrial protein.
Results: From a broad survey of land plants, we have found that the orf-bryo1 gene is also conserved in the mitochondria of vascular plants and charophycean green algae. This gene is actively transcribed and RNA edited in many flowering plants. Comparative sequence …
Prediction Of Antigenic Epitopes On Protein Surfaces By Consensus Scoring, Shide Liang, Dandan Zheng, Chi Zhang, Martin Zacharias
Prediction Of Antigenic Epitopes On Protein Surfaces By Consensus Scoring, Shide Liang, Dandan Zheng, Chi Zhang, Martin Zacharias
Center for Plant Science Innovation: Faculty and Staff Publications
Background: Prediction of antigenic epitopes on protein surfaces is important for vaccine design. Most existing epitope prediction methods focus on protein sequences to predict continuous epitopes linear in sequence. Only a few structure-based epitope prediction algorithms are available and they have not yet shown satisfying performance.
Results: We present a new antigen Epitope Prediction method, which uses ConsEnsus Scoring (EPCES) from six different scoring functions - residue epitope propensity, conservation score, sidechain energy score, contact number, surface planarity score, and secondary structure composition. Applied to unbounded antigen structures from an independent test set, EPCES was able to predict antigenic eptitopes …
The Majority Of The Type Iii Effector Inventory Of Pseudomonas Syringae Pv. Tomato Dc3000 Can Suppress Plant Immunity, Ming Guo, Fang Tian, Yashitola Wamboldt, James R. Alfano
The Majority Of The Type Iii Effector Inventory Of Pseudomonas Syringae Pv. Tomato Dc3000 Can Suppress Plant Immunity, Ming Guo, Fang Tian, Yashitola Wamboldt, James R. Alfano
Center for Plant Science Innovation: Faculty and Staff Publications
The Pseudomonas syringae type III protein secretion system (T3SS) and the type III effectors it injects into plant cells are required for plant pathogenicity and the ability to elicit a hypersensitive response (HR). The HR is a programmed cell death that is associated with effector-triggered immunity (ETI). A primary function of P. syringae type III effectors appears to be the suppression of ETI and pathogen-associated molecular pattern–triggered immunity (PTI), which is induced by conserved molecules on microorganisms. We reported that seven type III effectors from P. syringae pv. tomato DC3000 were capable of suppressing an HR induced by P. fluorescens …
A Dedicated Thioesterase Of The Hotdog-Fold Family Is Required For The Biosynthesis Of The Naphthoquinone Ring Of Vitamin K1, Joshua R. Widhalm, Chloë Van Oostende, Fabienne Furt, Gilles J. C. Basset
A Dedicated Thioesterase Of The Hotdog-Fold Family Is Required For The Biosynthesis Of The Naphthoquinone Ring Of Vitamin K1, Joshua R. Widhalm, Chloë Van Oostende, Fabienne Furt, Gilles J. C. Basset
Center for Plant Science Innovation: Faculty and Staff Publications
Phylloquinone (vitamin K1) is a bipartite molecule that consists of a naphthoquinone ring attached to a phytyl side chain. The coupling of these 2 moieties depends on the hydrolysis of the CoA thioester of 1,4-dihydroxy-2-naphthoate (DHNA), which forms the naphthalenoid backbone. It is not known whether such a hydrolysis is enzymatic or chemical. In this study, comparative genomic analyses identified orthologous genes of unknown function that in most species of cyanobacteria cluster with predicted phylloquinone biosynthetic genes. The encoded approximately 16-kDa proteins display homology with some Hotdog domain-containing CoA thioesterases that are involved in the catabolism of 4-hydroxybenzoyl-CoA …
Participation Of Leaky Ribosome Scanning In Protein Dual Targeting By Alternative Translation Initiation In Higher Plants, Yashitola Wamboldt, Saleem Mohammed, Christian Elowsky, Chris Wittgren, Wilson B. M. De Paula, Sally Ann Mackenzie
Participation Of Leaky Ribosome Scanning In Protein Dual Targeting By Alternative Translation Initiation In Higher Plants, Yashitola Wamboldt, Saleem Mohammed, Christian Elowsky, Chris Wittgren, Wilson B. M. De Paula, Sally Ann Mackenzie
Center for Plant Science Innovation: Faculty and Staff Publications
Postendosymbiotic evolution has given rise to proteins that are multiply targeted within the cell. Various mechanisms have been identified to permit the expression of proteins encoding distinct N termini from a single gene. One mechanism involves alternative translation initiation (aTI). We previously showed evidence of aTI activity within the Arabidopsis thaliana organellar DNA polymerase gene POLg2. Translation initiates at four distinct sites within this gene, two non-AUG, to produce distinct plastid and mitochondrially targeted forms of the protein. To understand the regulation of aTI in higher plants, we used Polg2 as a model to investigate both cis- and trans …
The 2008 Update Of The Aspergillus Nidulans Genome Annotation: A Community Effort, Jennifer Russo Wortman, Steven D. Harris, Geoffrey Turner, Aspergillus Nidulans Consortium
The 2008 Update Of The Aspergillus Nidulans Genome Annotation: A Community Effort, Jennifer Russo Wortman, Steven D. Harris, Geoffrey Turner, Aspergillus Nidulans Consortium
Center for Plant Science Innovation: Faculty and Staff Publications
The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional …
The Spitzenkörper: A Signalling Hub For The Control Of Fungal Development?, Steven D. Harris
The Spitzenkörper: A Signalling Hub For The Control Of Fungal Development?, Steven D. Harris
Center for Plant Science Innovation: Faculty and Staff Publications
In Aspergillus nidulans, asexual development culminates in the formation of a multicellular conidiophore that bears spores known as conidia. Although several factors required for conidiophore formation have been characterized, the mechanisms underlying the transition from vegetative growth to development remain obscure. However, the recent characterization of two of these factors, FlbB and FlbE, provides important new insight. Notably, these studies suggest that the Spitzenkörper (i.e. apical body), which is known to regulate hyphal morphogenesis, might also serve as a signalling hub that co-ordinates development transitions.
Protein-Protein Interactions Of Tandem Affinity Purified Protein Kinases From Rice, Jai S. Rohila, Mei Chen, Shuo Chen, Johann Chen, Ronald L. Cerny, Christopher Dardick, Patrick Canlas, Hiroaki Fujii, Michael Gribskov, Siddhartha Kanrar, Lucas Knoflicek, Becky Stevenson, Mingtang Xie, Xia Xu, Xianwu Zheng, Jing-Kang Zhu, Pamela Ronald, Michael E. Fromm
Protein-Protein Interactions Of Tandem Affinity Purified Protein Kinases From Rice, Jai S. Rohila, Mei Chen, Shuo Chen, Johann Chen, Ronald L. Cerny, Christopher Dardick, Patrick Canlas, Hiroaki Fujii, Michael Gribskov, Siddhartha Kanrar, Lucas Knoflicek, Becky Stevenson, Mingtang Xie, Xia Xu, Xianwu Zheng, Jing-Kang Zhu, Pamela Ronald, Michael E. Fromm
Center for Plant Science Innovation: Faculty and Staff Publications
Eighty-eight rice (Oryza sativa) cDNAs encoding rice leaf expressed protein kinases (PKs) were fused to a Tandem Affinity Purification tag (TAP-tag) and expressed in transgenic rice plants. The TAP-tagged PKs and interacting proteins were purified from the T1 progeny of the transgenic rice plants and identified by tandem mass spectrometry. Forty-five TAPtagged PKs were recovered in this study and thirteen of these were found to interact with other rice proteins with a high probability score. In vivo phosphorylated sites were found for three of the PKs. A comparison of the TAP-tagged data from a combined analysis of 129 …
Effectors, Effectors Et Encore Des Effectors: The Xiv International Congress On Molecular-Plant Microbe Interactions, Quebec, Jonathan D. Walton, Tyler J. Avis, James R. Alfano, Mark Gijzen, Pietro Spanu, Kim Hammond-Kosack, Federico Sánchez
Effectors, Effectors Et Encore Des Effectors: The Xiv International Congress On Molecular-Plant Microbe Interactions, Quebec, Jonathan D. Walton, Tyler J. Avis, James R. Alfano, Mark Gijzen, Pietro Spanu, Kim Hammond-Kosack, Federico Sánchez
Center for Plant Science Innovation: Faculty and Staff Publications
The IS-MPMI held its fourteenth meeting in Quebec City July 19-23, 2009. There were 956 attendees from 49 countries. Just over 50% of the participants were students or postdoctoral associates. Hani Antoun (Université Laval, Canada) served as Program Chair, capably assisted by the Local Organizing Committee and the IS-MPMI International Advisory Board. There were eight plenary sessions, 18 concurrent sessions, and over 700 posters.
Histone H3 Phosphorylation: Universal Code Or Lineage Specific Dialects?, Heriberto Cerutti, J. Armando Casas-Mollano
Histone H3 Phosphorylation: Universal Code Or Lineage Specific Dialects?, Heriberto Cerutti, J. Armando Casas-Mollano
Center for Plant Science Innovation: Faculty and Staff Publications
Post-translational modifications of histones modulate the functional landscape of chromatin and impinge on many DNA-mediated processes. Phosphorylation of histone H3 plays a role in the regulation of gene expression and in chromosome condensation/segregation. Certain evolutionarily conserved residues on histone H3—namely Thr3, Ser10, Thr11, and Ser28—are phosphorylated during interphase or mitosis in both metazoa and plants. However, many of the kinases involved in these events appear to have evolved independently in different lineages. Likewise, the mechanistic function of specific phosphorylated amino acids, although poorly understood, also seems to differ among eukaryotes. Moreover, some modifications, such as phosphorylation of histone H3 Ser10, …
7tmrmine: A Web Server For Hierarchical Mining Of 7tmr Proteins, Guoqing Lu, Zhifang Wang, Alan M. Jones, Etsuko N. Moriyama
7tmrmine: A Web Server For Hierarchical Mining Of 7tmr Proteins, Guoqing Lu, Zhifang Wang, Alan M. Jones, Etsuko N. Moriyama
Center for Plant Science Innovation: Faculty and Staff Publications
Background: Seven-transmembrane region-containing receptors (7TMRs) play central roles in eukaryotic signal transduction. Due to their biomedical importance, thorough mining of 7TMRs from diverse genomes has been an active target of bioinformatics and pharmacogenomics research. The need for new and accurate 7TMR/GPCR prediction tools is paramount with the accelerated rate of acquisition of diverse sequence information. Currently available and often used protein classification methods (e.g., profile hidden Markov Models) are highly accurate for identifying their membership information among already known 7TMR subfamilies. However, these alignment-based methods are less effective for identifying remote similarities, e.g., identifying proteins from highly divergent or possibly …
Intergenic Transcription By Rna Polymerase Ii Coordinates Pol Iv And Pol V In Sirna-Directed Transcriptional Gene Silencing In Arabidopsis, Binglian Zheng, Zhengming Wang, Shengben Li, Bin Yu, Jin -Yuan Liu, Xuemei Chen
Intergenic Transcription By Rna Polymerase Ii Coordinates Pol Iv And Pol V In Sirna-Directed Transcriptional Gene Silencing In Arabidopsis, Binglian Zheng, Zhengming Wang, Shengben Li, Bin Yu, Jin -Yuan Liu, Xuemei Chen
Center for Plant Science Innovation: Faculty and Staff Publications
Intergenic transcription by RNA Polymerase II (Pol II) is widespread in plant and animal genomes, but the functions of intergenic transcription or the resulting noncoding transcripts are poorly understood. Here, we show that Arabidopsis Pol II is indispensable for endogenous siRNA-mediated transcriptional gene silencing (TGS) at intergenic low-copy-number loci, despite the presence of two other polymerases—Pol IV and Pol V—that specialize in TGS through siRNAs. We show that Pol II produces noncoding scaffold transcripts that originate outside of heterochromatic, siRNA-generating loci. Through these transcripts and physical interactions with the siRNA effector protein ARGONAUTE4 (AGO4), Pol II recruits AGO4/siRNAs to homologous …
Roadmap For Future Research On Plant Pathogen Effectors, James R. Alfano
Roadmap For Future Research On Plant Pathogen Effectors, James R. Alfano
Center for Plant Science Innovation: Faculty and Staff Publications
Bacterial and eukaryotic plant pathogens deliver effector proteins into plant cells to promote pathogenesis. Bacterial pathogens containing type III protein secretion systems are known to inject many of these effectors into plant cells. More recently, oomycete pathogens have been shown to possess a large family of effectors containing the RXLR motif, and many effectors are also being discovered in fungal pathogens. Although effector activities are largely unknown, at least a subset suppress plant immunity. A plethora of new plant pathogen genomes that will soon be available thanks to next-generation sequencing technologies will allow the identification of many more effectors. This …