Genome-wide identification and expression analysis of the molecular chaperone binding protein BiP genes in Citrus

Guimarães, Roney Fontes; Camillo, Luciana; Sousa, Aurizângela Oliveira de; Gonçalves, Luana Pereira; Macedo, Jamilly Costa Cardoso; Siqueira, Giovano Sousa; Barbosa, Antônia Marlene Magalhães; Alvim, Fátima Cerqueira; Costa, Márcio Gilberto Cardoso; Pirovani, Carlos Priminho

doi:10.1007/s11295-018-1306-5

Cited by 3 publications

(2 citation statements)

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“…Therefore, the characterization of BiPs is a crucial contribution to the understanding of cellular, tissuespecific and developmentally related responses to ER stress. The BiP gene family has been investigated in several plant species, including Arabidopsis, rice, wheat, pepper and citrus 36,37,[41][42][43][44] . In addition, there are several historic and recent studies using transgenic lines overexpressing various BiPs to characterize their roles in plant tolerance to adverse environmental conditions or demonstrating some evidence for tissue specific regulation 6,15,32,36,43,45 .…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and characterization ofSolanum tuberosum BiPgenes reveals the role of the promoter architecture in BiP gene diversity

Herath

Gayral

Adhikari

et al. 2020

Preprint

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max)The endoplasmic reticulum (ER) immunoglobulin binding proteins (BiPs) are molecular chaperones involved in normal protein maturation and refolding malformed proteins through the unfolded protein response (UPR). Plants BiPs belong to a multi-gene family contributing to development, immunity, and responses to environmental stresses. This study identified three BiP homologues in the Solanum tuberosum (potato) genome using phylogenetic, amino acid sequence, 3-D protein modeling and gene structure analysis. These analyses revealed that StBiP1 and StBiP2 grouped with AtBiP2, whereas StBiP3 grouped with AtBiP3. While the protein sequences and folding structures are highly similar, these StBiPs are distinguishable by their expression patterns in different tissues and in response to environmental stressors such as treatment with heat, chemicals, or virus elicitors of UPR. Ab initio promoter analysis revealed that potato and Arabidopsis BiP1 and BiP2 promoters were highly enriched with cis regulatory elements (CREs) linked to developmental processes, whereas BiP3 promoters were enriched with stress-related CREs. The frequency and linear distribution of these CREs produced two phylogenetic branches that further resolve the groups identified through gene phylogeny and exon/intron phase analysis. These data reveal that the CRE architecture of BiP promoters potentially define their spatio -temporal expression patterns under developmental and stress related cues. IntroductionThe ER binding immunoglobulin protein (BiP), also known as the glucose receptor protein 78 (GRP78) is conserved across evolutionary kingdoms and is one of the best characterized molecular chaperones in the endoplasmic reticulum (ER). BiP guides the cotranslational translocation of nascent proteins into the ER, chaperones protein folding and maturation. BiP plays a key role in protein quality control by identifying and refolding misfolded proteins. BiP directs the post-translational translocation of proteins out of the ER. BiP contains an N-terminal nucleotide-binding domain (NBD) and a C-terminal substrate-binding domain (SBD). The NBD consists of two lobes surrounding the allosteric ATP-binding site, which modulates the substrate-binding activities. SBD consists of two subdomains, SBDβ and SBDα, which enable BiP to bind the hydrophobic surfaces of newly translated proteins to protect them from aggregation in an ATP-dependent manner. The SBDβ is a pocket with two primary loops that surround the nascent polypeptide and, the SBDα lid is covering this pocket 1 . All BiP proteins have C-terminal HDEL or KDEL signaling motif, which ensures their retention and function in the ER and an ATP-binding domain near the N-terminus 2 .Across eukaryotes, BiPs are among the most abundant chaperones in the ER and are directly engaged in regulating the unfolded protein response (UPR). Under normal conditions in mammalian cells, BiP binds to and inhibits the three ER stress sensors, protein kinase RNA-like ER kinase (PERK), activating transcription factor 6 (ATF6), and in...

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Section: Discussionmentioning

confidence: 99%

Genome-wide identification and characterization ofSolanum tuberosum BiPgenes reveals the role of the promoter architecture in BiP gene diversity

Herath

Gayral

Adhikari

et al. 2020

Preprint

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“…Another report in Capsicum annuum L. identified three genes encoding BiP proteins; CaBiP1, CaBiP2 and CaBiP3, where CaBiP1 overexpression in Arabidopsis thaliana was found to aid plant tolerance to salt, osmotic and drought stress ( Wang H. et al, 2017 ). Recently, research in citrus species reported the presence of CsBiP1 and CsBiP2 genes and showed that under drought stress the expression of CsBiP1 is upregulated in C. limonia , and CsBiP2 was observed to be upregulated in C. sinensis seedlings under cold and osmotic stress ( Guimarães et al, 2018 ), an interesting observation that offers a unique opportunity to study the regulation and role of BiP on different stresses. A similar observation has been made on Solanum tuberosum , where three candidates BiPs; StBiP1, StBiP2, and StBiP3 have been identified and only StBiP3 is upregulated under salt stress ( Herath et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

The Endoplasmic Reticulum Role in the Plant Response to Abiotic Stress

Reyes-Impellizzeri

Moreno

2021

Front. Plant Sci.

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The endoplasmic reticulum (ER) is the organelle where one third of the proteins of a cell are synthetized. Several of these proteins participate in the signaling and response of cells, tissues, or from the organism to the environment. To secure the proper synthesis and folding of these proteins, or the disposal of unfolded or misfolded proteins, the ER has different mechanisms that interact and regulate each other. These mechanisms are known as the ER quality control (ERQC), ER-associated degradation (ERAD) and the unfolded protein response (UPR), all three participants of the maintenance of ER protein homeostasis or proteostasis. Given the importance of the client proteins of these ER mechanisms in the plant response to the environment, it is expected that changes or alterations on their components have an impact on the plant response to environmental cues or stresses. In this mini review, we focus on the impact of the alteration of components of ERQC, ERAD and UPR in the plant response to abiotic stresses such as drought, heat, osmotic, salt and irradiation. Also, we summarize findings from recent publications looking for a connection between these processes and their possible client(s) proteins. From this, we observed that a clear connection has been established between the ERAD and UPR mechanisms, but evidence that connects ERQC components to these both processes or their possible client(s) proteins is still lacking. As a proposal, we suggest the use of proteomics approaches to uncover the identity of these proteins and their connection with ER proteostasis.

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Genome-wide identification and characterization of Solanum tuberosum BiP genes reveal the role of the promoter architecture in BiP gene diversity

Herath

Gayral²,

Adhikari

et al. 2020

Sci Rep

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The endoplasmic reticulum (ER) immunoglobulin binding proteins (BiPs) are molecular chaperones involved in normal protein maturation and refolding malformed proteins through the unfolded protein response (UPR). Plant BiPs belong to a multi-gene family contributing to development, immunity, and responses to environmental stresses. This study identified three BiP homologs in the Solanum tuberosum (potato) genome using phylogenetic, amino acid sequence, 3-D protein modeling, and gene structure analysis. These analyses revealed that StBiP1 and StBiP2 grouped with AtBiP2, whereas StBiP3 grouped with AtBiP3. While the protein sequences and folding structures are highly similar, these StBiPs are distinguishable by their expression patterns in different tissues and in response to environmental stressors such as treatment with heat, chemicals, or virus elicitors of UPR. Ab initio promoter analysis revealed that potato and Arabidopsis BiP1 and BiP2 promoters were highly enriched with cis-regulatory elements (CREs) linked to developmental processes, whereas BiP3 promoters were enriched with stress related CREs. The frequency and linear distribution of these CREs produced two phylogenetic branches that further resolve the groups identified through gene phylogeny and exon/intron phase analysis. These data reveal that the CRE architecture of BiP promoters potentially define their spatio-temporal expression patterns under developmental and stress related cues.

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Genome-wide identification and expression analysis of the molecular chaperone binding protein BiP genes in Citrus

Cited by 3 publications

References 47 publications

Genome-wide identification and characterization ofSolanum tuberosum BiPgenes reveals the role of the promoter architecture in BiP gene diversity

Genome-wide identification and characterization ofSolanum tuberosum BiPgenes reveals the role of the promoter architecture in BiP gene diversity

The Endoplasmic Reticulum Role in the Plant Response to Abiotic Stress

Genome-wide identification and characterization of Solanum tuberosum BiP genes reveal the role of the promoter architecture in BiP gene diversity

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