Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant

Abstract Fiber mutants are unique and valuable resources for understanding the genetic and molecular mechanisms controlling initiation and development of cotton fibers that are extremely elongated single epidermal cells protruding from the seed coat of cottonseeds. In this study, we reported a new fuzzless-tufted cotton mutant (Gossypium hirsutum) and showed that fuzzless-tufted near-isogenic lines (NILs) had similar agronomic traits and a higher ginning efficiency compared to their recurrent parents with normal fuzzy seeds. Genetic analysis revealed that the mutant phenotype is determined by a single incomplete dominant locus, designated N5. The mutation was fine mapped to an approximately 250-kb interval containing 33 annotated genes using a combination of bulked segregant sequencing, SNP chip genotyping, and fine mapping. Comparative transcriptomic analysis using 0–6 days post-anthesis (dpa) ovules from NILs segregating for the phenotypes of fuzzless-tufted (mutant) and normal fuzzy cottonseeds (wild-type) uncovered candidate genes responsible for the mutant phenotype. It also revealed that the flanking region of the N5 locus is enriched with differentially expressed genes (DEGs) between the mutant and wild-type. Several of those DEGs are members of the gene families with demonstrated roles in cell initiation and elongation, such as calcium-dependent protein kinase and expansin. The transcriptome landscape of the mutant was significantly reprogrammed in the 6 dpa ovules and, to a less extent, in the 0 dpa ovules, but not in the 2 and 4 dpa ovules. At both 0 and 6 dpa, the reprogrammed mutant transcriptome was mainly associated with cell wall modifications and transmembrane transportation, while transcription factor activity was significantly altered in the 6 dpa mutant ovules. These results imply a similar molecular basis for initiation of lint and fuzz fibers despite certain differences.

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Tau accumulation induces synaptic impairment and memory deficit by calcineurin-mediated inactivation of nuclear CaMKIV/CREB signaling

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1604519113 ◽

2016 ◽

Vol 113 (26) ◽

pp. E3773-E3781 ◽

Cited By ~ 69

Author(s):

Yaling Yin ◽

Di Gao ◽

Yali Wang ◽

Zhi-Hao Wang ◽

Xin Wang ◽

...

Keyword(s):

Molecular Mechanisms ◽

Camp Response Element Binding ◽

Memory Deficit ◽

Nuclear Fraction ◽

Wild Type ◽

Calcium Dependent ◽

Calcium Calmodulin Dependent ◽

Dependent Protein

Intracellular accumulation of wild-type tau is a hallmark of sporadic Alzheimer’s disease (AD), but the molecular mechanisms underlying tau-induced synapse impairment and memory deficit are poorly understood. Here we found that overexpression of human wild-type full-length tau (termed hTau) induced memory deficits with impairments of synaptic plasticity. Both in vivo and in vitro data demonstrated that hTau accumulation caused remarkable dephosphorylation of cAMP response element binding protein (CREB) in the nuclear fraction. Simultaneously, the calcium-dependent protein phosphatase calcineurin (CaN) was up-regulated, whereas the calcium/calmodulin-dependent protein kinase IV (CaMKIV) was suppressed. Further studies revealed that CaN activation could dephosphorylate CREB and CaMKIV, and the effect of CaN on CREB dephosphorylation was independent of CaMKIV inhibition. Finally, inhibition of CaN attenuated the hTau-induced CREB dephosphorylation with improved synapse and memory functions. Together, these data indicate that the hTau accumulation impairs synapse and memory by CaN-mediated suppression of nuclear CaMKIV/CREB signaling. Our findings not only reveal new mechanisms underlying the hTau-induced synaptic toxicity, but also provide potential targets for rescuing tauopathies.

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Genome-Wide Identification and Characterization of Calcium-Dependent Protein Kinase (CDPK) and CDPK-Related Kinase (CRK) Gene Families in Medicago truncatula

International Journal of Molecular Sciences ◽

10.3390/ijms22031044 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1044

Author(s):

Pengcheng Zhao ◽

Yajie Liu ◽

Weiyi Kong ◽

Jiayi Ji ◽

Tianyu Cai ◽

...

Keyword(s):

Protein Kinase ◽

Medicago Truncatula ◽

Purifying Selection ◽

Gene Families ◽

Segmental Duplications ◽

Dependent Protein Kinase ◽

Calcium Dependent ◽

Dependent Protein ◽

Calcium Dependent Protein Kinase

Calcium-dependent protein kinase (CDPK or CPK) and CDPK-related kinase (CRK) play an important role in plant growth, development, and adaptation to environmental stresses. However, their gene families had been yet inadequately investigated in Medicago truncatula. In this study, six MtCRK genes were computationally identified, they were classified into five groups with MtCDPKs based on phylogenetic relationships. Six pairs of segmental duplications were observed in MtCDPK and MtCRK genes and the Ka/Ks ratio, an indicator of selection pressure, was below 0.310, indicating that these gene pairs underwent strong purifying selection. Cis-acting elements of morphogenesis, multiple hormone responses, and abiotic stresses were predicted in the promoter region. The spatial expression of MtCDPKs and MtCRKs displays diversity. The expression of MtCDPKs and MtCRKs could be regulated by various stresses. MtCDPK4, 14, 16, 22, and MtCRK6 harbor both N-myristoylation site and palmitoylation site and were anchored on plasma membrane, while MtCDPK7, 9, and 15 contain no or only one N-acylation site and were distributed in cytosol and nucleus, suggesting that the N-terminal acylation sites play a key role in subcellular localization of MtCDPKs and MtCRKs. In summary, comprehensive characterization of MtCDPKs and MtCRKs provide a subset of candidate genes for further functional analysis and genetic improvement against drought, cold, salt and biotic stress.

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Characterization of a cyclic AMP-resistant Chinese hamster ovary cell mutant containing both wild-type and mutant species of type I regulatory subunit of cyclic AMP-dependent protein kinase.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(17)38665-9 ◽

1985 ◽

Vol 260 (26) ◽

pp. 13927-13933 ◽

Cited By ~ 15

Author(s):

T J Singh ◽

J Hochman ◽

R Verna ◽

M Chapman ◽

I Abraham ◽

...

Keyword(s):

Cyclic Amp ◽

Chinese Hamster ◽

Ovary Cell ◽

Regulatory Subunit ◽

Type I ◽

Wild Type ◽

Cell Mutant ◽

Dependent Protein Kinase ◽

Dependent Protein

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Humic acid enhances heat stress tolerance via transcriptional activation of Heat-Shock Proteins in Arabidopsis

Scientific Reports ◽

10.1038/s41598-020-71701-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Joon-Yung Cha ◽

Sang-Ho Kang ◽

Imdad Ali ◽

Sang Cheol Lee ◽

Myung Geun Ji ◽

...

Keyword(s):

Heat Stress ◽

Humic Acid ◽

Heat Shock ◽

Stress Tolerance ◽

Transcriptional Activation ◽

Molecular Mechanisms ◽

Agronomic Traits ◽

Enrichment Analysis ◽

Gene Families ◽

Heat Stress Tolerance

Abstract Humic acid (HA) is composed of a complex supramolecular association and is produced by humification of organic matters in soil environments. HA not only improves soil fertility, but also stimulates plant growth. Although numerous bioactivities of HA have been reported, the molecular evidences have not yet been elucidated. Here, we performed transcriptomic analysis to identify the HA-prompted molecular mechanisms in Arabidopsis. Gene ontology enrichment analysis revealed that HA up-regulates diverse genes involved in the response to stress, especially to heat. Heat stress causes dramatic induction in unique gene families such as Heat-Shock Protein (HSP) coding genes including HSP101, HSP81.1, HSP26.5, HSP23.6, and HSP17.6A. HSPs mainly function as molecular chaperones to protect against thermal denaturation of substrates and facilitate refolding of denatured substrates. Interestingly, wild-type plants grown in HA were heat-tolerant compared to those grown in the absence of HA, whereas Arabidopsis HSP101 null mutant (hot1) was insensitive to HA. We also validated that HA accelerates the transcriptional expression of HSPs. Overall, these results suggest that HSP101 is a molecular target of HA promoting heat-stress tolerance in Arabidopsis. Our transcriptome information contributes to understanding the acquired genetic and agronomic traits by HA conferring tolerance to environmental stresses in plants.

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Comparative Analysis of Calcium-Dependent Protein Kinase in Cucurbitaceae and Expression Studies in Watermelon

International Journal of Molecular Sciences ◽

10.3390/ijms20102527 ◽

2019 ◽

Vol 20 (10) ◽

pp. 2527 ◽

Cited By ~ 3

Author(s):

Chunhua Wei ◽

Ruimin Zhang ◽

Xiaozhen Yang ◽

Chunyu Zhu ◽

Hao Li ◽

...

Keyword(s):

Phylogenetic Trees ◽

Expression Patterns ◽

Gene Families ◽

Structural Variations ◽

Calcium Dependent ◽

Plot Analysis ◽

Expression Studies ◽

History Of ◽

Dependent Protein ◽

Male Flowers

Both the calcium-dependent protein kinases (CDPKs) and CDPK-related kinases (CRKs) play numerous roles in plant growth, development, and stress response. Despite genome-wide identification of both families in Cucumis, comparative evolutionary and functional analysis of both CDPKs and CRKs in Cucurbitaceae remain unclear. In this study, we identified 128 CDPK and 56 CRK genes in total in six Cucurbitaceae species (C. lanatus, C. sativus, C. moschata, C. maxima, C. pepo, and L. siceraria). Dot plot analysis indicated that self-duplication of conserved domains contributed to the structural variations of two CDPKs (CpCDPK19 and CpCDPK27) in C. pepo. Using watermelon genome as reference, an integrated map containing 25 loci (16 CDPK and nine CRK loci) was obtained, 16 of which (12 CDPK and four CRK) were shared by all seven Cucurbitaceae species. Combined with exon-intron organizations, topological analyses indicated an ancient origination of groups CDPK IV and CRK. Moreover, the evolutionary scenario of seven modern Cucurbitaceae species could also be reflected on the phylogenetic trees. Expression patterns of ClCDPKs and ClCRKs were studied under different abiotic stresses. Some valuable genes were uncovered for future gene function exploration. For instance, both ClCDPK6 and its ortholog CsCDPK14 in cucumber could be induced by salinity, while ClCDPK6 and ClCDPK16, as well as their orthologs in Cucumis, maintained high expression levels in male flowers. Collectively, these results provide insights into the evolutionary history of two gene families in Cucurbitaceae, and indicate a subset of candidate genes for functional characterizations in the future.

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