Identification of Cyclic Nucleotide Gated Channels Using Regular Expressions

Zelman, Alice K.; Dawe, Adam; Berkowitz, Gerald A.

doi:10.1007/978-1-62703-441-8_14

Cited by 16 publications

(36 citation statements)

References 43 publications

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“…in maize plant CNGCs and does not occur in the ion transporters found in other plants, such as rice, Arabidopsis, and tomato (Saand et al 2015b;Nawaz et al 2014;Zelman et al 2013). In this study, 12 ZmCNGCs were identified and the PBCs and hinge domains were highly conserved after alignment, which further confirmed the previous hypothesis (Saand et al 2015b) Manuscript to be reviewed 2013).…”

Section: Features and Evolution Of Plant Cngc Family Genessupporting

confidence: 86%

“…[FYL]-X- [LIVF], in the PBC and hinge region within the CNBD of CNGC proteins only exists in plant CNGCs and does not occur in other ion transporters (Zelman et al 2013;Saand et al 2015b).…”

Section: Introductionmentioning

confidence: 99%

“…The first plant CNGC was identified in Hordeum vulgare and named HvCBT1 (Schuurink et al 1998). The use of bioinformatics tools has led to the identification of the CNGC gene family members in Arabidopsis (20), rice (16) and other plants (18 in tomato and 26 in Brassica oleracea) (Bridges et al 2005;Nawaz et al 2014;Ward et al 2009;Zelman et al 2012;Saand et al 2015a;Chen et al 2015;Zelman et al 2013;Guo et al 2017;Kakar et al 2017). Manuscript to be reviewed have been characterized by genetic methods.…”

Section: Introductionmentioning

confidence: 99%

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Peer Review #2 of "Genome-wide identification and analysis of the CNGC gene family in maize (v0.3)"

2018

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As one of the non-selective cation channel gene families, the cyclic nucleotide-gated channel (CNGC) gene family plays a vital role in plant physiological processes that are related to signal pathways, plant development, and environmental stresses.However, genome-wide identification and analysis of the CNGC gene family in maize has not yet been undertaken. In the present study, twelve ZmCNGC genes were identified in the maize genome, which were unevenly distributed on chromosomes 1, 2, 4, 5, 6, 7, and 8. They were classified into five major groups, which were Groups I, II, III, IVa, and IVb. Phylogenetic analysis showed that gramineous plant CNGC genes expanded unequally during evolution. Group IV CNGC genes emerged first, whereas Groups I and II appeared later. Prediction analysis of cis-acting regulatory elements showed that 137 putative ciselements were related to hormone-response, abiotic stress, and organ development. Furthermore, 120 protein pairs were predicted to interact with the 12 ZmCNGC proteins and other maize proteins. The expression profiles of the ZmCNGC genes were expressed in tissue-specific patterns. These results provide important information that will increase our understanding of the CNGC gene family in maize and other plants.

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Section: Features and Evolution Of Plant Cngc Family Genessupporting

confidence: 86%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Peer Review #2 of "Genome-wide identification and analysis of the CNGC gene family in maize (v0.3)"

2018

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“…Individual plant CNGC genes were identified in several plant species including barley ( Schuurink et al, 1998 ), Arabidopsis ( Kohler et al, 1999 ; Kohler and Neuhaus, 2000 ) and tobacco ( Arazi et al, 1999 ). Genome-wide identification of CNGC gene family was also conducted in Arabidopsis ( Maser et al, 2001 ), rice ( Bridges et al, 2005 ), Populus trichocarpa ( Ward et al, 2009 ), pear ( Chen et al, 2015 ), a moss ( Physcomitrella patens ) and some algae ( Verret et al, 2010 ; Zelman et al, 2013 ). The Arabidopsis CNGC gene family is comprised of 20 members that are divided into groups I, II, III, IVa, and IVb according to their phylogenetic relationship ( Maser et al, 2001 ).…”

Section: Introductionmentioning

confidence: 99%

“…Recently, a plant CNGC-specific motif spanning the phosphate binding cassette (PBC) and hinge region within CNB domain of CNGC proteins is predicted. This motif identifies CNGCs but no other protein and thus represents an efficient tool to identify plant CNGCs, which has been validated in several species such as Arabidopsis , rice, P. patens and Selaginella moellendorffii ( Zelman et al, 2012 , 2013 ). Based on animal research, it has been suggested that plant CNGCs might conduct calcium.…”

Section: Introductionmentioning

confidence: 99%

Cyclic nucleotide gated channel gene family in tomato: genome-wide identification and functional analyses in disease resistance

Saand

Wen

et al. 2015

Front. Plant Sci.

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The cyclic nucleotide gated channel (CNGC) is suggested to be one of the important calcium conducting channels. Nevertheless, genome-wide identification and systemic functional analysis of CNGC gene family in crop plant species have not yet been conducted. In this study, we performed genome-wide identification of CNGC gene family in the economically important crop tomato (Solanum lycopersicum L.) and analyzed function of the group IVb SlCNGC genes in disease resistance. Eighteen CNGC genes were identified in tomato genome, and four CNGC loci that were misannotated at database were corrected by cloning and sequencing. Detailed bioinformatics analyses on gene structure, domain composition and phylogenetic relationship of the SlCNGC gene family were conducted and the group-specific feature was revealed. Comprehensive expression analyses demonstrated that SlCNGC genes were highly, widely but differently responsive to diverse stimuli. Pharmacological assays showed that the putative CNGC activators cGMP and cAMP enhanced resistance against Sclerotinia sclerotiorum. Silencing of group IVb SlCNGC genes significantly enhanced resistance to fungal pathogens Pythium aphanidermatum and S. sclerotiorum, strongly reduced resistance to viral pathogen Tobacco rattle virus, while attenuated PAMP- and DAMP-triggered immunity as shown by obvious decrease of the flg22- and AtPep1-elicited hydrogen peroxide accumulation in SlCNGC-silenced plants. Additionally, silencing of these SlCNGC genes significantly altered expression of a set of Ca2+ signaling genes including SlCaMs, SlCDPKs, and SlCAMTA3. Collectively, our results reveal that group IV SlCNGC genes regulate a wide range of resistance in tomato probably by affecting Ca2+ signaling.

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Genome-wide identification and functional analysis of the cyclic nucleotide-gated channel gene family in Chinese cabbage

Yang

Ren

et al. 2019

3 Biotech

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Cyclic nucleotide-gated channels (CNGCs) are a class of nonselective cationic channels that are widely found in animals and plants. Plant CNGCs participate in numerous biological functions that vary from development to stress tolerance. Most CNGC genes have been identified in plant genomes, but no such comprehensive study has yet been conducted on Chinese cabbage. In this study, thirty BrCNGC genes were identified, divided into five groups, and used for evolutionary analysis. We assigned names of all individual CNGC members on the basis of phylogenetic relationship with A. thaliana CNGCs. All BrCNGC genes were randomly distributed on chromosomes, and the A08 chromosome did not carry any CNGC gene. The CNGC genes of Chinese cabbage and A. thaliana from the same group displayed similar conserved motifs and gene structures. Especially the closer the homology, the higher the similarity. Quantitative expression analysis showed that most of the CNGC genes were expressed under four stresses, indicating that they play a key role in the stress response of Chinese cabbage. Expression patterns of 12 BrCNGC in the roots, stems, leaves, flowers, and siliques showed that BrCNGC8 and BrCNGC16 were specifically expressed only in flowers but not in other parts. This study lays a theoretical foundation for future research on the function of the CNGC gene family in Chinese cabbage.

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Identification of Cyclic Nucleotide Gated Channels Using Regular Expressions

Cited by 16 publications

References 43 publications

Peer Review #2 of "Genome-wide identification and analysis of the CNGC gene family in maize (v0.3)"

Peer Review #2 of "Genome-wide identification and analysis of the CNGC gene family in maize (v0.3)"

Cyclic nucleotide gated channel gene family in tomato: genome-wide identification and functional analyses in disease resistance

Genome-wide identification and functional analysis of the cyclic nucleotide-gated channel gene family in Chinese cabbage

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