Pectin, a highly abundant polysaccharide, is an important component of both primary and secondary cell walls, forming the main component of the middle lamella. The primary cell wall has an intricate structure composed of a complex network of cellulose microfibrils interconnected within a matrix of polysaccharides, including pectins, hemicelluloses, and glycoproteins. In addition, the cell wall is the primary interface for most plant-pathogen interactions, since it is the first physical barrier against invasion and infection. ![]() The plant cell wall plays an important role in various fundamental physiological processes of plant growth and development, such as maintaining the integrity of cellular content, morphogenesis, and cell signaling. ![]() The work is made available under the Creative Commons CC0 public domain dedication.ĭata Availability: The cloned sequences were deposited at NCBI with the accession numbers MK295632 and MK295633, and the peptide libraries were deposited at the proteomics data repository PRIDE Archive ( ) with the dataset identifier PXD012419.įunding: This work was supported by the FCT (Foundation for Science and Technology) postdoctoral fellowship SFRH/BPD/116030/2016 (to CSLV) the national project PTDC/AGR-PRO/2589/2014 – PratyTech (to MM), Biotechnology approaches towards control of the root lesion nematode Pratylenchus penetrans and by National Funds through FCT under the Project UID/AGR/00115/2013 (to CSLV and MM).Ĭompeting interests: The authors have declared that no competing interests exist. This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. Received: SeptemAccepted: FebruPublished: February 22, 2019 PLoS ONE 14(2):Įditor: Javier González-Miguel, Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), SPAIN To our knowledge, this is the first report on identification and characterization of a PME gene within the phylum Nematoda.Ĭitation: Vicente CSL, Nemchinov LG, Mota M, Eisenback JD, Kamo K, Vieira P (2019) Identification and characterization of the first pectin methylesterase gene discovered in the root lesion nematode Pratylenchus penetrans. The possible function and activity of the gene were assessed by transient expression of Pp-pme in plants of Nicotiana benthamiana plants via a Potato virus X-based vector. Temporal expression of Pp-pme in planta was validated at early time points of infection. penetrans as determined by in situ hybridization. Expression of the Pp-pme gene was localized in the esophageal glands of P. Both genomic and coding sequences of the gene were cloned for this species, that included the presence of four introns which eliminated a possible contamination from bacteria. Here we report the identification of a gene encoding a cell wall-degrading enzyme, pectin methylesterase PME (EC 3.1.1.11), in the root lesion nematode Pratylenchus penetrans. Many intrinsic bioinformatic issues are still present, e.g.Similar to other plant-parasitic nematodes, root lesion nematodes possess an array of enzymes that are involved in the degradation of the plant cell wall. However, severe challenges remain that are highlighted and discussed in this article these include: (i) robust false-positive assessment of peptide and protein identifications, (ii) complex protein inference against a background of highly redundant data, (iii) taxonomic and functional post-processing of identification data, and finally, (iv) the assessment and provision of metrics and tools for quantitative analysis. ![]() In particular, it focuses on the creation of tailored protein sequence databases, on the optimal use of database search algorithms including methods of error rate estimation, and finally on taxonomic and functional annotation of peptide and protein identifications.Įxpert opinion: Recently, various promising strategies and software tools have been proposed for handling typical data analysis issues in metaproteomics. This relatively young field aims to elucidate the functional and taxonomic interplay of proteins in microbiomes and its implications on human health and the environment.Īreas covered: This article reviews bioinformatics methods and software tools dedicated to the analysis of data from metaproteomics and metaproteogenomics experiments. Introduction: The study of microbial communities based on the combined analysis of genomic and proteomic data – called metaproteogenomics – has gained increased research attention in recent years.
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