Dataset Information

Bioinformatic indications that COPI- and clathrin-based transport systems are not present in chloroplasts: an Arabidopsis model.

ABSTRACT: Coated vesicle transport occurs in the cytosol of yeast, mammals and plants. It consists of three different transport systems, the COPI, COPII and clathrin coated vesicles (CCV), all of which participate in the transfer of proteins and lipids between different cytosolic compartments. There are also indications that chloroplasts have a vesicle transport system. Several putative chloroplast-localized proteins, including CPSAR1 and CPRabA5e with similarities to cytosolic COPII transport-related proteins, were detected in previous experimental and bioinformatics studies. These indications raised the hypothesis that a COPI- and/or CCV-related system may be present in chloroplasts, in addition to a COPII-related system. To test this hypothesis we bioinformatically searched for chloroplast proteins that may have similar functions to known cytosolic COPI and CCV components in the model plants Arabidopsis thaliana and Oryza sativa (subsp. japonica) (rice). We found 29 such proteins, based on domain similarity, in Arabidopsis, and 14 in rice. However, many components could not be identified and among the identified most have assigned roles that are not related to either COPI or CCV transport. We conclude that COPII is probably the only active vesicle system in chloroplasts, at least in the model plants. The evolutionary implications of the findings are discussed.

SUBMITTER: Lindquist E

PROVIDER: S-EPMC4138088 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:Preoperative mediastinal staging is crucial in the management of patients with non-small cell lung cancer (NSCLC), especially to define prognosis and the most proper treatment. To obtain the highest certainty level before lung resection, the current American and European guidelines for preoperative mediastinal nodal staging for NSCLC recommend getting tissue confirmation of regional nodal spread in all cases except in patients with small (?3 cm) peripheral carcinomas with no evidence of nodal involvement on computed tomography (CT) and positron emission tomography (PET). We have a wide variety of surgical methods for mediastinal staging that are well integrated in the current preoperative algorithms. Their main indication is the validation of negative results obtained by minimally invasive endoscopic techniques. However, recent studies have reported the superiority of mediastinoscopy over endosonography methods in terms of accuracy for those tumours classified as clinical (c) N0-1 by CT and PET or with intermediate risk of N2 disease (cN1 and central tumours). Apart from the exploration of the mediastinum, other surgical procedures [parasternal mediastinotomy, extended cervical mediastinoscopy (ECM) and video-assisted thoracoscopic surgery (VATS)] allow the completion of the staging process with the assessment of the primary tumour and metastasis, exploring the lung, pleural cavity, and pericardium when it is required. Transcervical lymphadenectomies represent the evolution of mediastinoscopy and they are already considered the most reliable method for mediastinal staging, mainly in the subgroup of patients in whom endosonography methods have a low sensitivity: tumours with normal mediastinum by CT and PET. In addition to their indication for staging, these procedures have also demonstrated to be feasible as preresectional lymphadenectomy in VATS lobectomy, improving the radicality of the number of lymph nodes and lymph node stations explored, mostly for left-sided tumours for which a complete mediastinal nodal dissection is not always possible by VATS approach.

Dataset Information

Bioinformatic indications that COPI- and clathrin-based transport systems are not present in chloroplasts: an Arabidopsis model.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets