Genome-wide identification of heat shock proteins in harpacticoid, cyclopoid, and calanoid copepods: Potential application in marine ecotoxicology

2021 ◽  
Vol 169 ◽  
pp. 112545
Author(s):  
Jun Chul Park ◽  
Jae-Seong Lee
Keyword(s):  
Heat Shock ◽  
Heat Shock Proteins ◽  
Potential Application ◽  
Calanoid Copepods ◽  
Genome Wide ◽  
Shock Proteins

scholarly journals Computational genome-wide identification of heat shock protein genes in the bovine genome

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1504 ◽  
Author(s):  
Oyeyemi O. Ajayi ◽  
Sunday O. Peters ◽  
Marcos De Donato ◽  
Sunday O. Sowande ◽  
Fidalis D.N. Mujibi ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Proteins ◽  
Bovine Genome ◽  
Protein Family ◽  
Evolutionary Trace ◽  
Sequence Identity ◽  
Genome Wide ◽  
Physico Chemical ◽  
Small Hsp ◽  
Shock Proteins

Background: Heat shock proteins (HSPs) are molecular chaperones known to bind and sequester client proteins under stress. Methods: To identify and better understand some of these proteins, we carried out a computational genome-wide survey of the bovine genome. For this, HSP sequences from each subfamily (sHSP, HSP40, HSP70 and HSP90) were used to search the Pfam (Protein family) database, for identifying exact HSP domain sequences based on the hidden Markov model. ProtParam tool was used to compute potential physico-chemical parameters detectable from a protein sequence. Evolutionary trace (ET) method was used to extract evolutionarily functional residues of a homologous protein family. Results: We computationally identified 67 genes made up of 10, 43, 10 and 4 genes belonging to small HSP, HSP40, HSP70 and HSP90 families respectively. These genes were widely dispersed across the bovine genome, except in chromosomes 24, 26 and 27, which lack bovine HSP genes. We found an uncharacterized outer dense fiber (ODF1) gene in cattle with an intact alpha crystallin domain, like other small HSPs. Physico-chemical characteristic of aliphatic index was higher in HSP70 and HSP90 gene families, compared to small HSP and HSP40. Grand average hydropathy showed that small HSP (sHSP), HSP40, HSP70 and HSP90 genes had negative values except for DNAJC22, a member of HSP40 gene family. The uniqueness of DNAJA3 and DNAJB13 among HSP40 members, based on multiple sequence alignment, evolutionary trace analysis and sequence identity dendrograms, suggests evolutionary distinct structural and functional features, with unique roles in substrate recognition and chaperone functions. The monophyletic pattern of the sequence identity dendrograms of cattle, human and mouse HSP sequences suggests functional similarities. Conclusions: Our computational results demonstrate the first-pass in-silico identification of heat shock proteins and calls for further investigation to better understand their functional roles and mechanisms in Bovidae.

scholarly journals Genome-wide analysis of heat shock proteins in C4 model, foxtail millet identifies potential candidates for crop improvement under abiotic stress

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Roshan Kumar Singh ◽  
Jananee Jaishankar ◽  
Mehanathan Muthamilarasan ◽  
Shweta Shweta ◽  
Anand Dangi ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Heat Shock ◽  
Heat Shock Proteins ◽  
Crop Improvement ◽  
Foxtail Millet ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Shock Proteins

scholarly journals Genome-wide identification of heat shock factors and heat shock proteins in response to UV and high intensity light stress in lettuce

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Taehoon Kim ◽  
Shafina Samraj ◽  
Juan Jiménez ◽  
Celina Gómez ◽  
Tie Liu ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Proteins ◽  
Light Stress ◽  
Stress Conditions ◽  
Heat Shock Factors ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Shock Proteins ◽  
High Intensity Light

Abstract Background Heat shock factors (Hsfs) and Heat shock proteins (Hsps) belong to an essential group of molecular regulators involved in controlling cellular processes under normal and stress conditions. The role of Hsfs and Hsps is well known in model plant species under diverse stress conditions. While plants Hsfs are vital components of the signal transduction response to maintain cellular homeostasis, Hsps function as chaperones helping to maintain folding of damaged and newly formed proteins during stress conditions. In lettuce (Lactuca sativa), a highly consumed vegetable crop grown in the field and in hydroponic systems, the role of these gene families in response to artificial light is not well characterized. Results Using a genome-wide analysis approach, we identified 32 Hsfs and 22 small heat shock proteins (LsHsps) in lettuce, some of which do not have orthologs in Arabidopsis, poplar, and rice. LsHsp60s, LsHsp90s, and LsHsp100s are highly conserved among dicot and monocot species. Surprisingly, LsHsp70s have three times more members than Arabidopsis and two times more than rice. Interestingly, the lettuce genome triplication did not contribute to the increased number of LsHsp70s genes. The large number of LsHsp70s was the result of genome tandem duplication. Chromosomal distribution analysis shows larger tandem repeats of LsHsp70s genes in Chr1, Chr7, Chr8, and Chr9. At the transcriptional level, some genes of the LsHsfs, LsHsps, LsHsp60s, and LsHsp70s families were highly responsive to UV and high intensity light stress, in contrast to LsHsp90s and LsHsp100s which did not respond to a light stimulus. Conclusions Our genome-wide analysis provides a detailed identification of Hsfs and Hsps in lettuce. Chromosomal location and syntenic region analysis together with our transcriptional analysis under different light conditions provide candidate genes for breeding programs aiming to produce lettuce varieties able to grow healthy under hydroponic systems that use artificial light.

scholarly journals Identification and characterization of developmental, tissue, and evolutionary transcription start sites in Bos taurus indicus

2020 ◽  
Author(s):  
Mehrnush Forutan ◽  
Elizabeth Ross ◽  
Amanda Chamberlain ◽  
Loan Nguyen ◽  
Brett Mason ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Proteins ◽  
Bos Taurus ◽  
Transcription Start Sites ◽  
Genome Wide ◽  
Bos Taurus Indicus ◽  
Shock Proteins ◽  
Inactive Genes ◽  
Transcriptional Start Sites

Abstract To further the understanding of the evolution of transcriptional regulation, we profiled genome-wide transcriptional start sites (TSSs) in two sub-species, Bos taurus taurus and Bos taurus indicus, that diverged approximately 500,000 years ago. Evolutionarily divergent TSSs were observed in more than half of the genes expressed across the sub-species, ranging from extreme cases in which a TSS was observed only in one sub-species to intermediate situations in which a corresponding TSS had been translocated by > 50 nucleotides, to situations where the number of TSS differed between the sub-species. Fetal and adult stages not only had their own regulatory profile of active and inactive genes but also their own pattern of TSSs. Given indicus are more adapted to heat, we also specifically investigated TSSs for heat shock proteins. More variation was observed in number of TSSs for heat shock proteins in indicus than taurus. This study confirmed that most genes are regulated in a tissue-specific manner.

scholarly journals Genome-wide identification of heat shock proteins (Hsps) and Hsp interactors in rice: Hsp70s as a case study

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 344 ◽  
Author(s):  
Yongfei Wang ◽  
Shoukai Lin ◽  
Qi Song ◽  
Kuan Li ◽  
Huan Tao ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Proteins ◽  
Genome Wide ◽  
Shock Proteins

scholarly journals Surveying the Lettuce Genome: Genome-wide Identification of Hsfs and Hsps in Response to UV and High Light Stress

2020 ◽  
Author(s):  
Taehoon Kim ◽  
Shafina Samraj ◽  
Juan Jimenez ◽  
Celina Gómez ◽  
Tie Liu ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Proteins ◽  
Light Stress ◽  
High Light ◽  
Artificial Light ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Hydroponic Systems ◽  
Shock Proteins

Abstract Background Heat shock factors (Hsfs) and Heat shock proteins (Hsps) belong to an essential group of molecular regulators involved in controlling cellular processes under normal and stress conditions. The role of Hsfs and Hsps is well known in model plant species under diverse stress conditions. However, in lettuce (Lactuca sativa), a highly consumed vegetable crop grown in the field and in hydroponic systems, the role of these gene families in response to artificial light is not well characterized. Results Using a genome-wide analysis approach, we identified 32 Hsfs and 22 small heat shock proteins (LsHsps) in lettuce, some of which do not have orthologous in Arabidopsis, poplar, and rice. LsHsp60s, LsHsp90s, and LsHsp100s are highly conserved among dicot and monocot species. Surprisingly, LsHsp70s have three times more members than Arabidopsis and two times more than rice. Genome triplication might have contributed to the increased number of LsHsp70s genes. Chromosomal distribution analysis shows larger tandem repeats of LsHsp70s genes in Chr1, Chr7, Chr8, and Chr9. At the transcriptional level, some genes of the LsHsfs, LsHsps, LsHsp60s, and LsHsp70s families were highly responsive to UV and high light stress, in contrast of LsHsp90s and LsHsp100s which did not respond to a light stimulus. Conclusions Our genome-wide analysis provides a detail identification of Hsfs and Hsps in lettuce. Chromosomal location and syntenic region analysis together with our transcriptional analysis under different light conditions provide candidate genes for breeding programs aiming to produce lettuce varieties able to grow healthy under hydroponic systems that use artificial light.

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