scholarly journals Phylogenetic comparison and splice site conservation of eukaryotic U1 snRNP-specific U1-70K gene family

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tao Fan ◽  
Yu-Zhen Zhao ◽  
Jing-Fang Yang ◽  
Qin-Lai Liu ◽  
Yuan Tian ◽  
...  
Keyword(s):  
Gene Family ◽  
Splice Site ◽  
Messenger Rna ◽  
Expression Patterns ◽  
Protein Structures ◽  
Single Copy ◽  
Central Component ◽  
Animal Kingdom ◽  
Functional Studies ◽  
U1 Snrnp

AbstractEukaryotic cells can expand their coding ability by using their splicing machinery, spliceosome, to process precursor mRNA (pre-mRNA) into mature messenger RNA. The mega-macromolecular spliceosome contains multiple subcomplexes, referred to as small nuclear ribonucleoproteins (snRNPs). Among these, U1 snRNP and its central component, U1-70K, are crucial for splice site recognition during early spliceosome assembly. The human U1-70K has been linked to several types of human autoimmune and neurodegenerative diseases. However, its phylogenetic relationship has been seldom reported. To this end, we carried out a systemic analysis of 95 animal U1-70K genes and compare these proteins to their yeast and plant counterparts. Analysis of their gene and protein structures, expression patterns and splicing conservation suggest that animal U1-70Ks are conserved in their molecular function, and may play essential role in cancers and juvenile development. In particular, animal U1-70Ks display unique characteristics of single copy number and a splicing isoform with truncated C-terminal, suggesting the specific role of these U1-70Ks in animal kingdom. In summary, our results provide phylogenetic overview of U1-70K gene family in vertebrates. In silico analyses conducted in this work will act as a reference for future functional studies of this crucial U1 splicing factor in animal kingdom.

scholarly journals Phylogenetic Comparison and Splicing Analysis of the U1 snRNP-specific Protein U1C in Eukaryotes

2021 ◽  
Vol 8 ◽  
Author(s):  
Kai-Lu Zhang ◽  
Jian-Li Zhou ◽  
Jing-Fang Yang ◽  
Yu-Zhen Zhao ◽  
Debatosh Das ◽  
...  
Keyword(s):  
Gene Family ◽  
Cancer Progression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Specific Protein ◽  
Comprehensive Overview ◽  
Small Nuclear Ribonucleoprotein ◽  
U1 Snrnp ◽  
Multiple Copies ◽  
And Function

As a pivotal regulator of 5’ splice site recognition, U1 small nuclear ribonucleoprotein (U1 snRNP)-specific protein C (U1C) regulates pre-mRNA splicing by interacting with other components of the U1 snRNP complex. Previous studies have shown that U1 snRNP and its components are linked to a variety of diseases, including cancer. However, the phylogenetic relationships and expression profiles of U1C have not been studied systematically. To this end, we identified a total of 110 animal U1C genes and compared them to homologues from yeast and plants. Bioinformatics analysis shows that the structure and function of U1C proteins is relatively conserved and is found in multiple copies in a few members of the U1C gene family. Furthermore, the expression patterns reveal that U1Cs have potential roles in cancer progression and human development. In summary, our study presents a comprehensive overview of the animal U1C gene family, which can provide fundamental data and potential cues for further research in deciphering the molecular function of this splicing regulator.

Genome-Wide Characterization of PDI Gene Family in Medicago truncatula and their Roles in Response to ER stress

Genome ◽  
2020 ◽  
Author(s):  
Zhe Meng ◽  
Yuwei Zhao ◽  
Lijie Liu ◽  
Xihua Du
Keyword(s):  
Protein Folding ◽  
Er Stress ◽  
Gene Family ◽  
Medicago Truncatula ◽  
Environmental Changes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Protein Structures ◽  
Pcr Analysis ◽  
Model Legume

Protein disulfide isomerases (PDIs) are pivotal protein folding catalysts in the endoplasmic reticulum (ER) through formation of disulfide bond, isomerization, and inhibition of misfolded protein aggregation. When protein folding capacity is overwhelmed by the demands during transitions between growth phases or under environmental changes, the accumulation of unfolded or misfolded proteins in the ER triggers ER stress. However, little is known about PDI gene family in the model legume, Medicago truncatula, especially the responses to ER stress. Therefore, we identified 17 putative PDIs from the genome of M. truncatula and presented their gene and protein structures, phylogenetic relationships, chromosomal distributions, and synteny analysis with the orthologs in other four eudicot species inculding A. thaliana, G. max, B. rapa, and V. vinifera. Moreover, expression profiles derived from transcriptome data showed distinct expression patterns of MtPDI genes among plant organs, while real-time quantitative PCR analysis and data from the proteome revealed the potential roles of MtPDIs in response to ER stress. Our study provides a foundation for further investigations of the biological roles of PDIs in Medicago, especially their roles in response to ER stress.

scholarly journals Genome-Wide Investigation of the NAC Gene Family and Its Potential Association with the Secondary Cell Wall in Moso Bamboo

Biomolecules ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 609 ◽  
Author(s):  
Shan ◽  
Yang ◽  
Xu ◽  
Zhu ◽  
Gao
Keyword(s):  
Cell Wall ◽  
Gene Family ◽  
Secondary Cell Wall ◽  
Expression Patterns ◽  
Wood Property ◽  
Moso Bamboo ◽  
Functional Studies ◽  
Bamboo Shoots ◽  
Potential Association ◽  
Nac Gene Family

NAC (NAM, ATAF, and CUC) transcription factors (TFs) are implicated in the transcriptional regulation of diverse processes and have been characterized in a number of plant species. However, NAC TFs are still not well understood in bamboo, especially their potential association with the secondary cell wall (SCW). Here, 94 PeNACs were identified and characterized in moso bamboo (Phyllostachys edulis). Based on their gene structures and conserved motifs, the PeNACs were divided into 11 groups according to their homologs in Arabidopsis. PeNACs were expressed variously in different tissues of moso bamboo, suggesting their functional diversity. Fifteen PeNACs associated with the SCW were selected for co-expression analysis and validation. It was predicted that 396 genes were co-expressed with the 15 PeNACs, in which 16 and 55 genes were involved in the lignin catabolic process and cellulose biosynthetic process respectively. As the degree of lignification in the growing bamboo shoots increased, all 15 PeNACs were upregulated with a trend of rising first and then decreasing except PeNAC37, which increased continuously. These results indicated that these PeNACs might play important roles in SCW biosynthesis and lignification in bamboo shoots. Seven of 15 PeNACs had been found positively co-expressed with seven PeMYBs, and they had similar expression patterns with those of the PeMYBs in bamboo shoots. The targeted sites of miR164 were found in 16 PeNACs, of which three PeNACs associated with SCW were validated to have an opposite expression trend to that of miR164 in growing bamboo shoots. In addition, three PeNACs were selected and verified to have self-activation activities. These results provide comprehensive information of the NAC gene family in moso bamboo, which will be helpful for further functional studies of PeNACs to reveal the molecular regulatory mechanisms of bamboo wood property.

scholarly journals Genome-wide identification and expression analysis of SWEET gene family in Litchi chinensis reveal the involvement of LcSWEET2a/3b in early seed development

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Hanhan Xie ◽  
Dan Wang ◽  
Yaqi Qin ◽  
Anna Ma ◽  
Jiaxin Fu ◽  
...  
Keyword(s):  
Gene Family ◽  
Seed Development ◽  
Expression Patterns ◽  
Phloem Loading ◽  
Reproductive Organs ◽  
Phylogenetic Tree Analysis ◽  
Multiple Sequence ◽  
Litchi Chinensis ◽  
Functional Studies ◽  
Early Seed Development

Abstract Background SWEETs (Sugar Will Eventually be Exported transporters) function as sugar efflux transporters that perform diverse physiological functions, including phloem loading, nectar secretion, seed filling, and pathogen nutrition. The SWEET gene family has been identified and characterized in a number of plant species, but little is known about in Litchi chinensis, which is an important evergreen fruit crop. Results In this study, 16 LcSWEET genes were identified and nominated according to its homologous genes in Arabidopsis and grapevine. Multiple sequence alignment showed that the 7 alpha-helical transmembrane domains (7-TMs) were basically conserved in LcSWEETs. The LcSWEETs were divided into four clades (Clade I to Clade IV) by phylogenetic tree analysis. A total of 8 predicted motifs were detected in the litchi LcSWEET genes. The 16 LcSWEET genes were unevenly distributed in 9 chromosomes and there was one pairs of segmental duplicated events by synteny analysis. The expression patterns of the 16 LcSWEET genes showed higher expression levels in reproductive organs. The temporal and spatial expression patterns of LcSWEET2a and LcSWEET3b indicated they play central roles during early seed development. Conclusions The litchi genome contained 16 SWEET genes, and most of the genes were expressed in different tissues. Gene expression suggested that LcSWEETs played important roles in the growth and development of litchi fruits. Genes that regulate early seed development were preliminarily identified. This work provides a comprehensive understanding of the SWEET gene family in litchi, laying a strong foundation for further functional studies of LcSWEET genes and improvement of litchi fruits.

scholarly journals The Soybean Laccase Gene Family: Evolution and Possible Roles in Plant Defense and Stem Strength Selection

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 701 ◽  
Author(s):  
Wang ◽  
Li ◽  
Zheng ◽  
Zhu ◽  
Ma ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Wild Soybean ◽  
Constitutive Expression ◽  
Gene Family Evolution ◽  
Laccase Gene ◽  
Functional Studies ◽  
Stem Strength ◽  
A Genome ◽  
Laccase Genes

Laccase is a widely used industrial oxidase for food processing, dye synthesis, paper making, and pollution remediation. At present, laccases used by industries come mainly from fungi. Plants contain numerous genes encoding laccase enzymes that show properties which are distinct from that of the fungal laccases. These plant-specific laccases may have better potential for industrial purposes. The aim of this work was to conduct a genome-wide search for the soybean laccase genes and analyze their characteristics and specific functions. A total of 93 putative laccase genes (GmLac) were identified from the soybean genome. All 93 GmLac enzymes contain three typical Cu-oxidase domains, and they were classified into five groups based on phylogenetic analysis. Although adjacent members on the tree showed highly similar exon/intron organization and motif composition, there were differences among the members within a class for both conserved and differentiated functions. Based on the expression patterns, some members of laccase were expressed in specific tissues/organs, while some exhibited a constitutive expression pattern. Analysis of the transcriptome revealed that some laccase genes might be involved in providing resistance to oomycetes. Analysis of the selective pressures acting on the laccase gene family in the process of soybean domestication revealed that 10 genes could have been under artificial selection during the domestication process. Four of these genes may have contributed to the transition of the soft and thin stem of wild soybean species into strong, thick, and erect stems of the cultivated soybean species. Our study provides a foundation for future functional studies of the soybean laccase gene family.

scholarly journals MicroRNAs in Diabetic Kidney Disease

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Rong Li ◽  
Arthur C. K. Chung ◽  
Xueqing Yu ◽  
Hui Y. Lan
Keyword(s):  
Kidney Disease ◽  
Messenger Rna ◽  
Diabetic Kidney Disease ◽  
Target Genes ◽  
Therapeutic Potential ◽  
Expression Patterns ◽  
Diagnostic Tools ◽  
Diabetic Kidney ◽  
Functional Studies ◽  
Gene Expression Studies

Rapid growth of diabetes and diabetic kidney disease exerts a great burden on society. Owing to the lack of effective treatments for diabetic kidney disease, treatment relies on drugs that either reduces its progression or involve renal replacement therapies, such as dialysis and kidney transplantation. It is urgent to search for biomarkers for early diagnosis and effective therapy. The discovery of microRNAs had lead to a new era of post-transcriptional regulators of gene expression. Studies from cells, experimental animal models and patients under diabetic conditions demonstrate that expression patterns of microRNAs are altered during the progression of diabetic kidney disease. Functional studies indicate that the ability of microRNAs to bind 3′ untranslated region of messenger RNA not only shows their capability to regulate expression of target genes, but also their therapeutic potential to diabetic kidney disease. The presence of microRNAs in plasma, serum, and urine has been shown to be possible biomarkers in diabetic kidney disease. Therefore, identification of the pathogenic role of microRNAs possesses an important clinical impact in terms of prevention and treatment of progression in diabetic kidney disease because it allows us to design novel and specific therapies and diagnostic tools for diabetic kidney disease.

scholarly journals Developmental and functional studies of the SLC12 gene family members from Drosophila melanogaster

2010 ◽  
Vol 298 (1) ◽  
pp. C26-C37 ◽  
Author(s):  
Qifei Sun ◽  
E. Tian ◽  
R. James Turner ◽  
Kelly G. Ten Hagen
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Family ◽  
Expression Patterns ◽  
Family Members ◽  
Specific Inhibitor ◽  
Insect Cell Line ◽  
Experimental Conditions ◽  
Functional Studies ◽  
Half Saturation Constant ◽  
Late Embryogenesis

The electroneutral cation-chloride cotransporter gene family, SLC12, contains nine members in vertebrates. These include seven sodium and/or potassium-coupled chloride transporters and two membrane proteins of unknown function. Although SLC12 family members have been identified in a number of lower species, the functional properties of these proteins are unknown. There are five SLC12 homologues in Drosophila melanogaster , including at least one member on each of the four main branches of the vertebrate phylogenetic tree. We have employed in situ hybridization to study the expression patterns of the Drosophila SLC12 proteins during embryonic development. Our studies indicate that all five members of this family are expressed during early embryogenesis ( stages 1–6), but that spatial and temporal expression patterns become more refined as development proceeds. Expression during late embryogenesis was seen predominantly in the ventral nerve cord, salivary gland, gut, and anal pad. In parallel studies, we have carried out transport assays on each of the five Drosophila homologues, expressed as recombinant proteins in the cultured insect cell line High Five. Under our experimental conditions, we found that only one of these proteins, CG4357, transported the potassium congener 86Rb. Additional experiments established that rubidium transport via CG4357 was saturable ( Km = 0.29 ± 0.05 mM), sodium-dependent (half-saturation constant = 53 ± 11 mM), chloride-dependent (half-saturation constant = 48 ± 5 mM), and potently inhibited by bumetanide (inhibitor constant = 1.17 ± 0.08 μM), a specific inhibitor of Na+-K+-2Cl− cotransporters. Taken together, our results provide strong evidence that CG4357 is an insect ortholog of the vertebrate Na+-K+-2Cl− cotransporters.

scholarly journals Birth-and-death evolution of the fatty acyl-CoA reductase (FAR) gene family and diversification of cuticular hydrocarbon synthesis in Drosophila

2019 ◽  
Author(s):  
Cédric Finet ◽  
Kailey Slavik ◽  
Jian Pu ◽  
Sean B. Carroll ◽  
Henry Chung
Keyword(s):  
Fatty Acid ◽  
Gene Family ◽  
Cuticular Hydrocarbon ◽  
Evolutionary Model ◽  
Gene Families ◽  
Single Copy ◽  
Fatty Acyl ◽  
Comparative Approach ◽  
Hydrocarbon Synthesis ◽  
Functional Studies

AbstractThe birth-and-death evolutionary model proposes that some members of a multigene family are phylogenetically stable and persist as a single copy over time whereas other members are phylogenetically unstable and undergo frequent duplication and loss. Functional studies suggest that stable genes are likely to encode essential functions, while rapidly evolving genes reflect phenotypic differences in traits that diverge rapidly among species. One such class of rapidly diverging traits are insect cuticular hydrocarbons (CHCs), which play dual roles in chemical communications as short-range recognition pheromones as well as protecting the insect from desiccation. Insect CHCs diverge rapidly between related species leading to ecological adaptation and/or reproductive isolation. Because the CHC and essential fatty acid biosynthetic pathways share common genes, we hypothesized that genes involved in the synthesis of CHCs would be evolutionary unstable, while those involved in fatty acid-associated essential functions would be evolutionary stable. To test this hypothesis, we investigated the evolutionary history of the fatty acyl-CoA reductases (FARs) gene family that encodes enzymes in CHC synthesis. We compiled a unique dataset of 200 FAR proteins across 12 Drosophila species. We uncovered a broad diversity in FAR content which is generated by gene duplications, subsequent gene losses, and alternative splicing. We also show that FARs expressed in oenocytes and presumably involved in CHC synthesis are more unstable than FARs from other tissues. We suggest that a comparative approach investigating the birth-and-death evolution of gene families can identify candidate genes involved in rapidly diverging traits between species.

scholarly journals Structure of a transcribing RNA polymerase II–U1 snRNP complex

Science ◽  
2021 ◽  
Vol 371 (6526) ◽  
pp. 305-309 ◽  
Author(s):  
Suyang Zhang ◽  
Shintaro Aibara ◽  
Seychelle M. Vos ◽  
Dmitry E. Agafonov ◽  
Reinhard Lührmann ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Splice Site ◽  
Messenger Rna ◽  
Loop Formation ◽  
Mrna Isoforms ◽  
Pol Ii ◽  
Small Nuclear Ribonucleoprotein ◽  
Starting Point ◽  
U1 Snrnp

To initiate cotranscriptional splicing, RNA polymerase II (Pol II) recruits the U1 small nuclear ribonucleoprotein particle (U1 snRNP) to nascent precursor messenger RNA (pre-mRNA). Here, we report the cryo–electron microscopy structure of a mammalian transcribing Pol II–U1 snRNP complex. The structure reveals that Pol II and U1 snRNP interact directly. This interaction positions the pre-mRNA 5′ splice site near the RNA exit site of Pol II. Extension of pre-mRNA retains the 5′ splice site, leading to the formation of a “growing intron loop.” Loop formation may facilitate scanning of nascent pre-mRNA for the 3′ splice site, functional pairing of distant intron ends, and prespliceosome assembly. Our results provide a starting point for a mechanistic analysis of cotranscriptional spliceosome assembly and the biogenesis of mRNA isoforms by alternative splicing.

scholarly journals Mechanism of 5ʹ splice site transfer for human spliceosome activation

Science ◽  
2019 ◽  
Vol 364 (6438) ◽  
pp. 362-367 ◽  
Author(s):  
Clément Charenton ◽  
Max E. Wilkinson ◽  
Kiyoshi Nagai
Keyword(s):  
Splice Site ◽  
Messenger Rna ◽  
Catalytic Center ◽  
U6 Snrna ◽  
Dead Box ◽  
Cryo Electron Microscopy ◽  
Branch Point Sequence ◽  
U1 Snrnp ◽  
Spliceosome Activation ◽  
Small Nuclear Ribonucleoproteins

The prespliceosome, comprising U1 and U2 small nuclear ribonucleoproteins (snRNPs) bound to the precursor messenger RNA 5ʹ splice site (5ʹSS) and branch point sequence, associates with the U4/U6.U5 tri-snRNP to form the fully assembled precatalytic pre–B spliceosome. Here, we report cryo–electron microscopy structures of the human pre–B complex captured before U1 snRNP dissociation at 3.3-angstrom core resolution and the human tri-snRNP at 2.9-angstrom resolution. U1 snRNP inserts the 5ʹSS–U1 snRNA helix between the two RecA domains of the Prp28 DEAD-box helicase. Adenosine 5ʹ-triphosphate–dependent closure of the Prp28 RecA domains releases the 5ʹSS to pair with the nearby U6 ACAGAGA-box sequence presented as a mobile loop. The structures suggest that formation of the 5ʹSS-ACAGAGA helix triggers remodeling of an intricate protein-RNA network to induce Brr2 helicase relocation to its loading sequence in U4 snRNA, enabling Brr2 to unwind the U4/U6 snRNA duplex to allow U6 snRNA to form the catalytic center of the spliceosome.

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