Genes In Different Species Research Articles

Comprehensive Genomic Analysis of G2-like Transcription Factor Genes and Their Role in Development and Abiotic Stresses in Arabidopsis

GOLDEN2-LIKE (GLK) transcription factors are a subfamily of GARP family transcription factors, which play an essential function in plant growth and development as well as stress response during abiotic and biotic stress conditions. This study reports GLK genes in the Arabidopsis thaliana genome in-depth and identified 55 AtGLK genes in the Arabidopsis genome. Phylogenetic analyses resolved these GLK gene clusters into seven groups. A Ka/Ks ratios analysis indicated that they had experienced purifying selection. Many essential cis elements are present in the promoter regions of AtGLK genes associated with plant hormones, light, and stress. The expression profile from RNA-Seq data revealed that 29.1% of them had relatively high expression in all tested tissues or organs, indicating their crucial housekeeping function in plant growth and development. However, many other GLK members were selectively expressed in particular tissues or organs. In silico study of the transcriptional regulation of AtGLKs indicated that it is strongly regulated by cold, drought, osmotic, salt, and metal ion stressors. Our research provides essential information for the functional studies of each GLK gene in different species in the future.

Application Progress of Dual RNA Sequencing in Microbial Research

The human body is colonized by densely-populated and structurally complex communities of microorganisms. The microbiota interact not only with their host cells, but also with other microbiota. Dual RNA sequencing (Dual RNA-seq) can be used to conduct simultaneous analysis of the dynamic changes of gene expression of two (or more) interactive species, and to obtain thus, through the interaction model diagram, the inter-species regulatory relationship of genes of different species, and hence the interaction mechanism between species. We herein reviewed the application status and development prospects of Dual RNA-seq in the research of intestinal, respiratory, skin and oral microbes. Since the concept of Dual RNA-seq was first introduced, the technology has been applied to a range of infection models. Direct investigation into the dynamic interactions between species at the molecular level will contribute to the better understanding of the physiological changes of pathogens and hosts during the course of infection, and thus help reveal potential new targets or biomarkers. However, the Dual RNA-seq technology is still in its early stage of development, and there are some limitations in the experimental technology. For example, due to the dynamic nature of the interaction between species, there are urgent problems awaiting solutions, such as the optimal experimental conditions, the selection of sampling sites and how to achieve real-time observation. In addition, due to the large amount of bioinformatics data of Dual RNA-seq, further research is needed to explore for ways to process the interaction information quickly and flexibly.

The SF3B1R625H mutation promotes prolactinoma tumor progression through aberrant splicing of DLG1

BackgroundRecently, a hotspot mutation in prolactinoma was observed in splicing factor 3b subunit 1 (SF3B1R625H), but its functional effects and underlying molecular mechanisms remain largely unexplored.MethodsUsing the CRISPR/Cas9 genome editing system and rat pituitary GH3 cells, we generated heterozygous Sf3b1R625H mutant cells. Sanger and whole-genome sequencing were conducted to verify the introduction of this mutation. Transcriptome analysis was performed in SF3B1-wild-type versus mutant human prolactinoma samples and GH3 cells. RT-PCR and minigene reporter assays were conducted to verify aberrant splicing. The functional consequences of SF3B1R625H were evaluated in vitro and in vivo. Critical makers of epithelial-mesenchymal transition and key components were detected using western blot, immunohistochemistry, and immunofluorescence. Suppressing proteins was achieved using siRNA.ResultsTranscriptomic analysis of prolactinomas and heterozygous mutant cells revealed that the SF3B1R625H allele led to different alterations in splicing properties, affecting different genes in different species. SF3B1R625H promoted aberrant splicing and DLG1 suppression in both rat cells and human tumors. In addition, SF3B1R625H and knocking down DLG1 promoted cell migration, invasion, and epithelial-mesenchymal transition through PI3K/Akt pathway.ConclusionsOur findings elucidate a mechanism through which mutant SF3B1 promotes tumor progression and may provide a potent molecular therapeutic target for prolactinomas with the SF3B1R625H mutation.

Sending out an SOS - the bacterial DNA damage response

The term “SOS response” was first coined by Radman in 1974, in an intellectual effort to put together the data suggestive of a concerted gene expression program in cells undergoing DNA damage. A large amount of information about this cellular response has been collected over the following decades. In this review, we will focus on a few of the relevant aspects about the SOS response: its mechanism of control and the stressors which activate it, the diversity of regulated genes in different species, its role in mutagenesis and evolution including the development of antimicrobial resistance, and its relationship with mobile genetic elements.

Review: Balancing Selection for Deleterious Alleles in Livestock.

Harmful alleles can be under balancing selection due to an interplay of artificial selection for the variant in heterozygotes and purifying selection against the variant in homozygotes. These pleiotropic variants can remain at moderate to high frequency expressing an advantage for favorable traits in heterozygotes, while harmful in homozygotes. The impact on the population and selection strength depends on the consequence of the variant both in heterozygotes and homozygotes. The deleterious phenotype expressed in homozygotes can range from early lethality to a slightly lower fitness in the population. In this review, we explore a range of causative variants under balancing selection including loss-of-function variation (i.e., frameshift, stop-gained variants) and regulatory variation (affecting gene expression). We report that harmful alleles often affect orthologous genes in different species, often influencing analogous traits. The recent discoveries are mainly driven by the increasing genomic and phenotypic resources in livestock populations. However, the low frequency and sometimes subtle effects in homozygotes prevent accurate mapping of such pleiotropic variants, which requires novel strategies to discover. After discovery, the selection strategy for deleterious variants under balancing selection is under debate, as variants can contribute to the heterosis effect in crossbred animals in various livestock species, compensating for the loss in purebred animals. Nevertheless, gene-assisted selection is a useful tool to decrease the frequency of the harmful allele in the population, if desired. Together, this review marks various deleterious variants under balancing selection and describing the functional consequences at the molecular, phenotypic, and population level, providing a resource for further study.

Computational modelling of chromosomally clustering protein domains in bacteria

BackgroundIn bacteria, genes with related functions—such as those involved in the metabolism of the same compound or in infection processes—are often physically close on the genome and form groups called clusters. The enrichment of such clusters over various distantly related bacteria can be used to predict the roles of genes of unknown function that cluster with characterised genes. There is no obvious rule to define a cluster, given their variability in size and intergenic distances, and the definition of what comprises a “gene”, since genes can gain and lose domains over time. Protein domains can cluster within a gene, or in adjacent genes of related function, and in both cases these are chromosomally clustered. Here, we model the distances between pairs of protein domain coding regions across a wide range of bacteria and archaea via a probabilistic two component mixture model, without imposing arbitrary thresholds in terms of gene numbers or distances.ResultsWe trained our model using matched gene ontology terms to label functionally related pairs and assess the stability of the parameters of the model across 14,178 archaeal and bacterial strains. We found that the parameters of our mixture model are remarkably stable across bacteria and archaea, except for endosymbionts and obligate intracellular pathogens. Obligate pathogens have smaller genomes, and although they vary, on average do not show noticeably different clustering distances; the main difference in the parameter estimates is that a far greater proportion of the genes sharing ontology terms are clustered. This may reflect that these genomes are enriched for complexes encoded by clustered core housekeeping genes, as a proportion of the total genes. Given the overall stability of the parameter estimates, we then used the mean parameter estimates across the entire dataset to investigate which gene ontology terms are most frequently associated with clustered genes.ConclusionsGiven the stability of the mixture model across species, it may be used to predict bacterial gene clusters that are shared across multiple species, in addition to giving insights into the evolutionary pressures on the chromosomal locations of genes in different species.

Comparative analysis of codon usage patterns of FUT2 from different species

Enterotoxigenic E. coli is an important zoonotic pathogen causing diarrhea in human and newborn animals. α - (1,2) fucosyltransferase 2 (FUT2) is closely associated with the formation of pathogenic receptors of Enterotoxigenic E. coli. Codon usage bias analysis can help to better understand the molecular mechanisms and evolutionary relationships of a particular gene. In order to understand the codon usage pattern of FUT2 gene, FUT2 gene coding sequences of nine species were selected from GenBank database for calculating the nucleotide composition (GC content) and genetic indices including effective number of codons, relative synonymous codon usage and relative codon usage bias using R software, in order to analyze codon usage bias and base composition in FUT2 gene from different species. The results showed that the codon usage of FUT2 gene in different species was affected by GC bias, especially GC frequency at the third position of codon (GC3). Most of the optimal codons were biased towards the G/C-ending types. GCC, CUG, UCC, GUG and AUC showed the highest relative synonymous codon usage value among different species, belonging to the most dominant codons. The usage characteristic of the codens for FUT2 gene in Sus scrofa was similar to that of Bos taurus; Homo sapiens was similar to Pan troglodytes. Effective number of codons was significantly, negatively correlated with GC3, and the relative higher frequency of optimal codon implied that FUT2 genes from different species had a strong bias in codon usage.

Expression of cupA gene cluster responsible for biofilm formation in Pseudomonas aeruginosa is enhanced against subinhibitory concentration of carbapenems

IntroductionPseudomonas aeruginosa, an opportunistic pathogen, is a potent biofilm forming organism. Independent of the type IV pili, the cupA cluster in Pseudomonas aeruginosa facilitates biofilm formation which provides protection against antibacterial treatment. The pel and psl genes synthesizing exopolysaccharides also initiate biofilm formation. Investigations revealed antibiotic exposure to be associated with modulated expression of many resistance genes in different species of bacteria depending upon the concentrations in which these are used. In recent days, the use of carbapenems, is growing at an alarming rate to treat infections and may also have a regulatory effect in the expression of cupA, pslA and pelA genes associated with biofilm formation. The present study therefore was taken up to investigate the possible role of carbapenem on these gene's expression at sub lethal dose. MethodologySix carbapenem non susceptible isolates of Pseudomonas aeruginosa of clinical origin were selected for the study. The isolates were cultured upto log phase in fresh Luria Bertani broth with and without 2 μg/ml imipenem and meropenem respectively and the transcriptional response of the cupA1, cupA2, cupA3, cupA4,cupA5, pelA and pslA genes in the isolates were studied by quantitative real time PCR using the ΔΔct method. ResultsThe analysis of transcriptional response of cupA1, cupA2, cupA3, cupA4,cupA5,pslA and pelA genes in the isolates revealed that the response was enhanced multiple folds under sub inhibitory concentration (2 μg/ml) imipenem and meropenem stress as compared to the response of the genes under normal growth condition i.e. without any antibiotic pressure. ConclusionThe present study could underscore the role of imipenem and meropenem at sub lethal dose and could infer that both imipenem and meropenem at sub lethal dose has a regulatory effect on the transcriptional response of cupA, pelA and pslA genes which are involved in biofilm formation.

In Silico Functional Prediction and Expression Analysis of C2H2 Zinc-Finger Family Transcription Factor Revealed Regulatory Role of ZmZFP126 in Maize Growth.

The C2H2-zinc finger proteins (ZFP) comprise a large family of transcription factors with various functions in biological processes. In maize, the function regulation of C2H2- zine finger (ZF) genes are poorly understood. We conducted an evolution analysis and functional prediction of the maize C2H2-ZF gene family. Furthermore, the ZmZFP126 gene has been cloned and sequenced for further favorable allelic variation discovery. The phylogenetic analysis of the C2H2-ZF domain indicated that the position and sequence of the C2H2-ZF domain of the poly-zinc finger gene are relatively conserved during evolution, and the C2H2-ZF domain with the same position is highly conserved. The expression analysis of the C2H2-ZF gene family in 11 tissues at different growth stages of B73 inbred lines showed that genes with multiple transcripts were endowed with more functions. The expression analysis of the C2H2-ZF gene in P1 and P2 inbred lines under drought conditions showed that the C2H2-ZF genes were mainly subjected to negative regulation under drought stress. Functional prediction indicated that the maize C2H2-ZF gene is mainly involved in reproduction and development, especially concerning the formation of important agronomic traits in maize yield. Furthermore, sequencing and correlation analysis of the ZmZFP126 gene indicated that this gene was significantly associated with the SDW-NAP and TDW-NAP. The analysis of the relationship between maize C2H2-ZF genes and C2H2-ZF genes with known functions indicated that the functions of some C2H2-ZF genes are relatively conservative, and the functions of homologous genes in different species are similar.

The Application of CRISPR/Cas9 Technology for Farm Animals: A Review

Livestock animal are important for agriculture economy and biomedical research. They are sources of Milk, meat, carcass, organic manure and other products. The development of genome editing technologies, especially CRISPR-Cas have revolutionized the generation of gene edited farm animals. In this review, we briefly introduce the CRISPR-Cas9 technology and highlight its application on livestock such as human disease modeling, disease resistant animal, and generation of hornless cattle, animal welfare and other agricultural and biomedical related traits which enhance the livestock production in order to meet the increasing demand of food worldwide. The ability to transfer sperm-producing stem cells or spermatogonial stem cells (SSCs) from a donor animal into the testes of a recipient male could have multiple applications. Production of BLG free milk in cattle provides a promising way to those who have allergy to cow milk. The knockdown of myostatin gene in different species like Sheep, Goat, Cattle and pig is very helpful in the economy of meat industry. Besides the several benefits of CRISPR-Cas9 technology, the risk factors and ethics issues related to this technology should be reconsidered before they enter into CRISPR era.

Stability evaluation of reference genes for real-time quantitative PCR normalization in Spodoptera frugiperda (Lepidoptera: Noctuidae)

Real-time quantitative PCR (qPCR) is a reliable and widely used technique for analyzing the expression profiles of target genes in different species, and reference genes with stable expressions have been introduced for the normalization of the data. Therefore, stability evaluation should be considered as the initial step for qPCR experiments. The fall armyworm Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) is a polyphagous pest that consumes many plant species and seriously threatens corn production around the world. However, no studies thus far have examined the stability of reference genes in this pest. In this study, the expression profiles of the eight candidate reference genes of Actin, elongation factor 1 alpha (EF1α), elongation factor 2 (EF2), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ribosomal protein L3 (RPL3), ribosomal protein L13 (RPL13), alpha-tubulin (α-TUB), and beta-1-tubulin (β-1-TUB) were obtained from S. frugiperda in different samples and the stability was evaluated by ΔCt, BestKeeper, geNorm, NormFinder, and RefFinder methods. The results of pairwise variation (V) calculated by GeNorm indicated two reference genes could be selected for normalization. Therefore, the combinations of the most stable reference genes for different experimental conditions of S. frugiperda were shown as follows: EF2 and RPL13 for developmental stages, RPL3 and β-1-TUB for larval tissue samples, EF2 and EF1α for the larval samples treated with different temperatures, RPL3 and EF1α for the larval samples under starvation stress, and RPL13 and EF1α for all the samples. Our results lay the foundation for the normalization of qPCR analyses in S. frugiperda and could help guarantee the accuracy of subsequent research.

VvMYB114 mediated by miR828 negatively regulates trichome development of Arabidopsis

Trichome is a specialized structure differentiated during the morphogenesis of plant leaf epidermal cells. In recent years, with the continuous researches on trichome development of Arabidopsis and other plants, more and more genes related to trichome morphogenesis have been discovered, including R2R3-type MYB genes. In this study, we cloned a R2R3-type MYB family gene from grape, VvMYB114, a target gene of vvi-miR828. qRT-PCR showed that VvMYB114 mRNA accumulated during grape fruit ripening, and VvMYB114 protein had transcriptional activation activity. Heterologous overexpression of VvMYB114 in Arabidopsis reduced the number of trichome on leaves and stems. Mutating the miR828-binding site in VvMYB114 without altering amino-acid sequence had no effect on trichome development in Arabidopsis. The results showed a different role of the regulation of miR828 to VvMYB114 in Arabidopsis from in grape, which indicated the functional divergence of miRNA targeting homoeologous genes in different species played an important roles in evolution and useful trait selection.

Regeneration Roadmap: database resources for regenerative biology.

Regeneration plays an instrumental role in biological development and damage repair by constructing and replacing cells, tissues, and organs. Since regenerative capacity declines with age, promoting regeneration is heralded as a potential strategy for delaying aging. On this premise, mechanisms that regulate regeneration have been extensively studied across species and in different tissues. However, an open and comprehensive database collecting and standardizing the abundant data generated in regeneration research, such as high-throughput sequencing data, remains to be developed. In this work, we constructed Regeneration Roadmap to systematically and comprehensively collect such information over 2.38 million data entries across 11 species and 36 tissues, including regeneration-related genes, bulk and single-cell transcriptomics, epigenomics, and pharmacogenomics data. In this database, users can explore regulatory and expression changes of regeneration-associated genes in different species and tissues. Regeneration Roadmap provides the research community with a long-awaited and valuable data resource featuring convenient computing and visualizing tools, which is publicly available at https://ngdc.cncb.ac.cn/regeneration/index.

Phylogenetic Analysis of NHX1 Gene in Different Species of Plants Based on Coding Sequences

Abstract not available
 Plant Tissue Cult. & Biotech. 30(2): 307-313, 2020 (December)

Analysis of codon usage bias of chloroplast genes in Oryza species : Codon usage of chloroplast genes in Oryza species.

The codon usage bias in chloroplast genes of Oryza species was low and AT rich. The pattern of codon usage was different among Oryza species and mainly influenced by mutation pressure and natural selection. Codon usage bias (CUB) is the unequal usage of synonymous codons in which some codons are more preferred to others in the coding sequences of genes. It shows a species-specific property. We studied the patterns of codon usage and the factors that influenced the CUB of protein-coding chloroplast (cp) genes in 18 Oryza species as no work was yet reported. The nucleotide composition analysis revealed that the overall GC content of cp genes in different species of Oryza was lower than 50%, i.e., Oryza cp genes were AT rich. Synonymous codon usage order (SCUO) suggested that CUB was weak in the cp genes of different Oryza species. A highly significant correlation was observed between overall nucleotides and its constituents at the third codon position suggesting that both, mutation pressure and natural selection, might influence the CUB. Correspondence analysis (COA) revealed that codon usage pattern differed across Oryza species. In the neutrality plot, a narrow range of GC3 distribution was recorded and some points were diagonally distributed in all the plots, suggesting that natural selection and mutation pressure might have influenced the CUB. The slope of the regression line was < 0.5, augmenting our inference that natural selection might have played a major role, while mutation pressure had a minor role in shaping the CUB of cp genes. The magnitudes of mutation pressure and natural selection on cp genes varied across Oryza species.

Multilateral Bioinformatics Analyses Reveal the Function-Oriented Target Specificities and Recognition of the RNA-Binding Protein SFPQ.

SummaryRNA-binding proteins (RBPs) recognize consensus sequences and regulate specific target mRNAs. However, large-scale CLIP-seq revealed loose and broad binding of RBPs to larger proportion of expressed mRNAs: e.g. SFPQ binds to >10,000 pre-mRNAs but distinctly regulates <200 target genes during neuronal development. Identification of crucial binding for regulation and rules of target recognition is highly anticipated for systemic understanding of RBP regulations. For a breakthrough solution, we developed a bioinformatical method for CLIP-seq and transcriptome data by adopting iterative hypothesis testing. Essential binding was successfully identified in C-rich sequences close to the 5′ splice sites of long introns, which further proposed target recognition mechanism via association between SFPQ and splicing factors during spliceosome assembly. The identified features of functional binding enabled us to predict regulons and also target genes in different species. This multilateral bioinformatics approach facilitates the elucidation of functionality, regulatory mechanism, and regulatory networks of RBPs.

The Quest for Orthologs benchmark service and consensus calls in 2020

The identification of orthologs—genes in different species which descended from the same gene in their last common ancestor—is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous algorithms and resources have been conceived to address this problem, but benchmarking and interpreting them is fraught with difficulties (need to compare them on a common input dataset, absence of ground truth, computational cost of calling orthologs). To address this, the Quest for Orthologs consortium maintains a reference set of proteomes and provides a web server for continuous orthology benchmarking (http://orthology.benchmarkservice.org). Furthermore, consensus ortholog calls derived from public benchmark submissions are provided on the Alliance of Genome Resources website, the joint portal of NIH-funded model organism databases.

MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life.

Inferring homology relationships across genes in different species is a central task in comparative genomics. Therefore, a large number of resources and methods have been developed over the years. Some public databases include phylogenetic trees of homologous gene families which can be used to further differentiate homology relationships into orthology and paralogy. MetaPhOrs is a web server that integrates phylogenetic information from different sources to provide orthology and paralogy relationships based on a common phylogeny-based predictive algorithm and associated with a consistency-based confidence score. Here we describe the latest version of the web server which includes major new implementations and provides orthology and paralogy relationships derived from ∼8.2 million gene family trees—from 13 different source repositories across ∼4000 species with sequenced genomes. MetaPhOrs server is freely available, without registration, at http://orthology.phylomedb.org/

Flexibility and Adaptability of Quorum Sensing in Nature.

Quorum sensing (QS), a type of chemical communication, allows bacteria to sense and coordinate activities in natural biofilm communities using N-acyl homoserine lactones (AHLs) as one type of signaling molecule. For AHL-based communication to occur, bacteria must produce and recognize the same signals, which activate similar genes in different species. Our current understanding of AHL-QS suggests that signaling between species would arise randomly, which is not probable. We propose that AHL-QS signaling is a mutable and adaptable process, within limits. AHLs are highly-conserved signals, however, their corresponding receptor proteins (LuxR) are highly variable. We suggest that both flexibility and adaptation occur among receptor proteins, allowing for complex signaling networks to develop in biofilms over time.

Genome-wide identification and comprehensive study of anti-fungal genes in chickpea

Chickpea is an important crop that delivers nutritious food to the increasing global community and it will become increasingly popular as a result of climate change. Our objective was to use comprehensive data analysis to locate and identify candidate genes for fungal disease resistance. We used a comprehensive bioinformatics pipeline of sequence alignment, phylogenetic analysis, protein chemical and physical properties assessment and domain structure classification. In order to study gene evolution and genetic diversity, we compared these genes with known anti-fungal genes in different species of plants. A total of 19721 protein sequences belonging to 187 plant species have been downloaded from public databases, including the entire chickpea genome. We have successfully identified 23 potential anti-fungal genes in 10 different chromosomes and genomic scaffolds using sequence alignment and gene annotation. Ca2 and Ca6 have the highest number of genes followed by Ca3 and Ca4. Anti-fungal chickpea proteins have been identified as cysteine-rich (10), thaumatin (6), pathogenesis (4) and plasmodesmata (3) proteins. Analysis of the chemical and physical correlation of anti-fungal proteins revealed a high correlation between different aspects of anti-fungal proteins. Five different pattern patterns have been detected in the anti-fungal chickpea proteins identified, including domain families associated with fungal resistance. The maximum likelihood of phylogenetic analysis was successful in distinguishing between anti-fungal chickpea proteins as seen in their protein patterns/domains.