Identification of the key functional genes in salt-stress tolerance of Cyanobacterium Phormidium tenue using in silico analysis

The development of artificial biocrust using cyanobacterium Phormidium tenue has been suggested as an effective strategy to prevent soil degradation. Here, a combination of in silico approaches with growth rate, photosynthetic pigment, morphology, and transcript analysis was used to identify specific genes and their protein products in response to 500 mM NaCl in P. tenue. The results show that 500 mM NaCl induces the expression of genes encoding glycerol-3-phosphate dehydrogenase (glpD) as a Flavoprotein, ribosomal protein S12 methylthiotransferase (rimO), and a hypothetical protein (sll0939). The constructed co-expression network revealed a group of abiotic stress-responsive genes. Using the Basic Local Alignment Search Tool (BLAST), the homologous proteins of rimO, glpD, and sll0939 were identified in the P. tenue genome. Encoded proteins of glpD, rimO, and DUF1622 genes, respectively, contain (DAO and DAO C), (UPF0004, Radical SAM and TRAM 2), and (DUF1622) domains. The predicted ligand included 22B and MG for DUF1622, FS5 for rimO, and FAD for glpD protein. There was no direct disruption in ligand-binding sites of these proteins by Na+, Cl-, or NaCl. The growth rate, photosynthetic pigment, and morphology of P. tenue were investigated, and the result showed an acceptable tolerance rate of this microorganism under salt stress. The quantitative real-time polymerase chain reaction (qRT-PCR) results revealed the up-regulation of glpD, rimO, and DUF1622 genes under salt stress. This is the first report on computational and experimental analyses of the glpD, rimO, and DUF1622 genes in P. tenue under salt stress to the best of our knowledge.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03050-w.

Selection and validation of reference genes for RT-qPCR normalization in different tissues of milk thistle (Silybum marianum, Gaert.)

Quantitative reverse transcription PCR is a sensitive technique for evaluating transcriptional profiles in different experimental datasets. To obtain a reliable quantification of the transcripts level, data normalization with stable reference genes is required. Stable reference genes are identified after analysis of their transcripts profile in every new experiment and species of interest. In Silybum marianum, a widely cultivated officinal plant, only few gene expression studies exist, and reference genes for RT-qPCR studies in the diverse plant tissues have never been investigated before. In this work, the expression stability of 10 candidate reference genes was evaluated in leaves, roots, stems and fruits of S. marianum grown under physiological environmental condition. The stability values for each candidate reference gene were calculated by four canonical statistical algorithms GeNorm, NormFinder, Bestkeeper and ΔCt method in different subsets of samples, then they were ranked with RefFinder from the most to the least suitable for normalization. Best combinations of reference genes are finally proposed for different experimental data sets, including all tissues, vegetative, and reproductive tissues separately. Three target genes putatively involved in important biosynthetic pathway leading to key metabolites in the fruits of milk thistle, such as silymarin and fatty acids, were analyzed with the chosen panels of reference genes, in comparison to the ones used in previous papers. To the best of our knowledge, this is the first report on a reliable and systematic identification and validation of the reference genes for RT-qPCR normalization to study gene expression in S. marianum.

Study of Autophagy in Plant Senescence

As a major intracellular degradation pathway, autophagy contributes to nutrient recycling and is indispensable during plant senescence. Here we describe methods used for investigating the autophagic process during leaf senescence. These include transcript analysis of core machinery autophagy genes, immunoblotting of ATG8, and microscopic observation of autophagosome formation.

Effects of multi and selective targeted tyrosine kinase inhibitors on function and signaling of different bladder cancer cells

BACKGROUND

Signaling of receptor tyrosine kinases (RTK) is dysregulated in various malignancies including bladder cancer. RTKs trigger pro-proliferative, anti-apoptotic and metastatic signaling pathways. Here, we assessed the effects of a selective tyrosine kinase inhibitor (TKI) (BGJ398) targeting fibroblast growth factor receptor (FGFR) and a pan-TKI (TKI258) targeting (FGFR), platelet derived growth factor receptor (PDGFR) and vascular endothelial growth factor receptor (VEGFR) in bladder cancer cells.

METHODS

Levels of mRNA transcripts were measured in nine human cell lines by quantitative RT-PCR. Cell function was assessed for viability, colony formation, migration, apoptosis and proliferation. Protein mediators of signal transduction were measured by Western-blot.

RESULTS

mRNA transcripts encoding RTK-related components, transcription factors, epithelial and mesenchymal transition (EMT) markers as well as cell cycle and apoptotic factors were determined in the cell lines. Principal component analysis ordered one epithelial-like cell cluster (5637, BFTC-905, MGHU4, RT112) and one mesenchymal-like cell cluster (T24, UMUC3, HU456, TCC-SUP). Cell response scores towards TKI258 and BGJ398 treatment were heterogeneous between cell lines and correlated with certain transcript levels. Analysis of signal transduction pathways revealed inhibition of fibroblast growth factor receptor (FGFR) signaling and induction of cell cycle dependent kinase (CDKN1A, p21) in epithelial-like cells differing in this regard from responses to mesenchymal-like cells that exhibited inhibition of mitogen-activated protein kinase (MAPK).

CONCLUSION

RTK and EMT related transcript analysis separate bladder cancer cells in two clusters. Functional responses towards TKI258 and BGJ398 treatment of bladder Fcancer cells were heterogeneous with deviating effects on signaling and possibly different therapeutic outcome.

Characterization of genes specific to sua-CMS in Nicotiana tabacum

KEY MESSAGE

Six unique ORFs were characterized in tobacco plants with sua-CMS sterile cytoplasm, identifying the mtDNA basis for pollen sterility. sua-CMS (cytoplasmic male sterility), the most widely used sterile system in tobacco hybrids, is the only CMS type identified as having no negative effects on agronomic or quality traits in tobacco (Nicotiana tabacum) and as being fully male sterile. CMS is often associated with alterations of mitochondrial DNA (mtDNA), including novel chimeric open reading frames (ORFs), which result from rearrangement and recombination. Here, we obtained 34 mitochondrial ORFs in the sua-CMS line msZhongyan100 (sZY) by BLAST analysis. When we amplified these mitochondrial ORFs in seven tobacco CMS lines including sua-, glu-, rep-, rus-, tab1-, tab2-, and tab3-CMS types and in fertile tobacco, we found that six ORFs-orf82, orf103, orf115a, orf91, orf115b, and orf100-were located in three small regions (m-sr) of the mitochondrial genome of sZY and were unique to the sua-CMS line. We further amplified the m-sr fragments in three different backcross populations of the seven types of CMS, three F1 hybrids with sua-CMS sterile cytoplasm, two sua-CMS lines, and 284 fertile tobacco accessions. The ORFs were specific to plants with the sua-CMS background. All six unique ORFs were chimeric and had no homology with the mitochondrial genomes of fertile tobacco. Transcript analysis revealed that the ORFs were highly expressed in the anthers and floral buds of sZY. These six ORFs were specific to sua-CMS and could be used as molecular markers to identify sua-CMS lines, which is useful for improving breeding for heterosis in tobacco.

Transcript profiling of salt tolerant tobacco mutants generated via mutation breeding

The main aim of the study is to identify the genes differentially, predominantly or specifically expressed in salt tolerant tobacco mutants, improved from Akhisar 97 and İzmir Özbaş varieties via mutation breeding, with respect to unstressed control plants. Seven tobacco mutants which have different salt tolerance capacities were evaluated by Gene Fishing analysis. Under stress conditions differentially expressed 100 reproducible bands were identified (74 of up-regulated and 20 of down-regulated while 6 were unknown). 75 of differentially expressed genes (DEGs) were successfully extracted from the gel and sequence analyses were performed. Functional annotation of the DEGs was performed against Blastn by interrogating their sequences. The 65 salt-regulated differentially expressed genes showed similarity with known genes, while 6 of DEGs didn't show any genetic similarities with known genes. DEGs were classified in eleven functional categories involving the abiotic stress response, biotic stress response, energy metabolism, cellular transport, catalitic activity, protein modification, amino acid metabolism and transcription factors. All the mutants were evaluated for their regulatory mechanisms against salt stress. The current data reveal that these six DEGs should be identified by next generation sequencing techniques and functional analysis should be design to understand the role of these six differentially expressed genes of tobacco mutants in further studies to improve new genetic resources.

Mapping Plastid Transcript Population by Circular Reverse Transcription Polymerase Chain Reaction

During evolution of photosynthetic organisms, the genetic information provided by the internalized cyanobacteria has been transferred to the nucleus. The small genome kept by the chloroplast, the so-called plastome, displays a complex organization, comprising operons under the control of multiples promoters. In addition, polycistronic transcripts undergo multiple processing events, thus generating a complex population of mRNAs from a single gene. This chapter describes a method to investigate the diversity of the mRNA population from a single gene by circular RT-PCR. The protocol provided here allows for the simultaneous mapping of both 5' and 3' ends of the same RNA molecule.

Bayesian Analysis of RNA-Seq Data Using a Family of Negative Binomial Models

The analysis of RNA-Seq data has been focused on three main categories, including gene expression, relative exon usage and transcript expression. Methods have been proposed independently for each category using a negative binomial (NB) model. However, counts following a NB distribution on one feature (e.g., exon) do not guarantee a NB distribution for the other two features (e.g., gene/transcript). In this paper we propose a family of Negative Binomial models, which integrates the gene, exon and transcript analysis under a coherent NB model. The proposed model easily incorporates the uncertainty of assigning reads to transcripts and simplifies substantially the estimation for the relative usage. We developed simple Gibbs sampling algorithms for the posterior inference by exploiting fully tractable closed-forms of computation via suitable conjugate priors. The proposed models were investigated under extensive simulations. Finally, we applied our model to a real data set.

Cluster-Level Relationships of Genes Involved in Carbon Metabolism in Synechocystis sp. PCC 6803: Development of a Novel Succinate-Producing Strain

We quantified the transcript levels of 44 genes related to sugar catabolism in strains with altered primary carbon metabolism and discovered a consistent expression pattern among succinate-producing mutants. To identify factors that determine the expression pattern, we calculated Pearson's correlation coefficients, using the transcript data. Correlation analysis revealed positive and negative correlations among genes encoding sugar catabolic enzymes. On the basis of this analysis, we found that the mutant overexpressing both rre37 (encoding an OmpR-type response regulator) and sigE (encoding an RNA polymerase sigma factor) produced increased levels of succinate under dark, anaerobic conditions, with a maximum productivity of 420 mg l-1.

Splice Site Variants in the KCNQ1 and SCN5A Genes: Transcript Analysis as a Tool in Supporting Pathogenicity

BACKGROUND

Approximately 75% of clinically definite long QT syndrome (LQTS) cases are caused by mutations in the KCNQ1, KCNH2 and SCN5A genes. Of these mutations, a small proportion (3.2-9.2%) are predicted to affect splicing. These mutations present a particular challenge in ascribing pathogenicity.

METHODS

Here we report an analysis of the transcriptional consequences of two mutations, one in the KCNQ1 gene (c.781_782delinsTC) and one in the SCN5A gene (c.2437-5C>A), which are predicted to affect splicing. We isolated RNA from lymphocytes and used a directed PCR amplification strategy of cDNA to show mis-spliced transcripts in mutation-positive patients.

RESULTS

The loss of an exon in each mis-spliced transcript had no deduced effect on the translational reading frame. The clinical phenotype corresponded closely with genotypic status in family members carrying the KCNQ1 splice variant, but not in family members with the SCN5A splice variant. These results are put in the context of a literature review, where only 20% of all splice variants reported in the KCNQ1, KCNH2 and SCN5A gene entries in the HGMDPro 2015.4 database have been evaluated using transcriptional assays.

CONCLUSIONS

Prediction programmes play a strong role in most diagnostic laboratories in classifying variants located at splice sites; however, transcriptional analysis should be considered critical to confirm mis-splicing. Critically, this study shows that genuine mis- splicing may not always imply clinical significance, and genotype/phenotype cosegregation remains important even when mis-splicing is confirmed.

The genome-wide role of HSF-1 in the regulation of gene expression in Caenorhabditis elegans

BACKGROUND

The heat shock response, induced by cytoplasmic proteotoxic stress, is one of the most highly conserved transcriptional responses. This response, driven by the heat shock transcription factor HSF1, restores proteostasis through the induction of molecular chaperones and other genes. In addition to stress-dependent functions, HSF1 has also been implicated in various stress-independent functions. In C. elegans, the HSF1 homolog HSF-1 is an essential protein that is required to mount a stress-dependent response, as well as to coordinate various stress-independent processes including development, metabolism, and the regulation of lifespan. In this work, we have performed RNA-sequencing for C. elegans cultured in the presence and absence of hsf-1 RNAi followed by treatment with or without heat shock. This experimental design thus allows for the determination of both heat shock-dependent and -independent biological targets of HSF-1 on a genome-wide level.

RESULTS

Our results confirm that C. elegans HSF-1 can regulate gene expression in both a stress-dependent and -independent fashion. Almost all genes regulated by HS require HSF-1, reinforcing the central role of this transcription factor in the response to heat stress. As expected, major categories of HSF-1-regulated genes include cytoprotection, development, metabolism, and aging. Within both the heat stress-dependent and -independent gene groups, significant numbers of genes are upregulated as well as downregulated, demonstrating that HSF-1 can both activate and repress gene expression either directly or indirectly. Surprisingly, the cellular process most highly regulated by HSF-1, both with and without heat stress, is cuticle structure. Via network analyses, we identify a nuclear hormone receptor as a common link between genes that are regulated by HSF-1 in a HS-dependent manner, and an epidermal growth factor receptor as a common link between genes that are regulated by HSF-1 in a HS-independent manner. HSF-1 therefore coordinates various physiological processes in C. elegans, and HSF-1 activity may be coordinated across tissues by nuclear hormone receptor and epidermal growth factor receptor signaling.

CONCLUSION

This work provides genome-wide HSF-1 regulatory networks in C. elegans that are both heat stress-dependent and -independent. We show that HSF-1 is responsible for regulating many genes outside of classical heat stress-responsive genes, including genes involved in development, metabolism, and aging. The findings that a nuclear hormone receptor may coordinate the HS-induced HSF-1 transcriptional response, while an epidermal growth factor receptor may coordinate the HS-independent response, indicate that these factors could promote cell non-autonomous signaling that occurs through HSF-1. Finally, this work highlights the genes involved in cuticle structure as important HSF-1 targets that may play roles in promoting both cytoprotection as well as longevity.

Distribution analysis of profilin isoforms at transcript resolution with mRNA-seq and secondary structure in various organs of Rattus norvegicus

Profilin (Pfn) is an actin binding protein, ubiquitously found in mammals and is essential for the actin polymerization in cells. In brain, it plays a pivotal role in neurogenesis and synapse formation by interacting with various proteins. Four Pfn isoforms have been identified in mammals. This study presents the identification and transcriptional expression of various Pfn isoforms (Pfn1, Pfn2, Pfn3 and Pfn4) in brain, heart, kidney, liver, and muscle and testis of Rattus norvegicus. Organs have been classified into groups based on some similarities. Group I includes brain and testis, Group II includes skeletal muscle and heart, while Group III includes kidney and liver. Pfn1 has been identified in all groups, Pfn2 and Pfn3 have been identified in group I, group III and in one organ (skeletal muscle) of group II. To the best of the authors knowledge, no report of Pfn1 and Pfn2 presence in testis, Pfn3 in brain, liver and skeletal muscle, Pfn4 in kidney and skeletal muscle exists to date. Transcriptional expression showed variations among expression level of different Pfn isoforms in various organs with respect to the control gene GADPH. We hypothesize that this could be attributed to profilin isoform specific mRNA structure and corresponding motifs, which generally contribute to similar or varied decay rates, cellular localization, post transcriptional regulation pattern and ligand binding.

Regulation of cuticle formation during fruit development and ripening in 'Newhall' navel orange (Citrus sinensis Osbeck) revealed by transcriptomic and metabolomic profiling

Fruit cuticle, which is composed of cutin and wax and biosynthesized during fruit development, plays important roles in the prevention of water loss and the resistance to pathogen infection during fruit development and postharvest storage. However, the key factors and mechanisms regarding the cuticle biosynthesis in citrus fruits are still unclear. Here, fruit cuticle of 'Newhall' navel orange (Citrus sinensis Osbeck) was studied from the stage of fruit expansion to postharvest storage from the perspectives of morphology, transcription and metabolism. The results demonstrated that cutin accumulation is synchronous with fruit expansion, while wax synthesis is synchronous with fruit maturation. Metabolic profile of fruits peel revealed that transition of metabolism of fruit peel occurred from 120 to 150 DAF and ABA was predicted to regulate citrus wax synthesis during the development of Newhall fruits. RNA-seq analysis of the peel from the above two stages manifested that the genes involved in photosynthesis were repressed, while the genes involved in the biosynthesis of wax, cutin and lignin were significantly induced at later stages. Further real-time PCR predicted that MYB transcription factor GL1-like regulates citrus fruits wax synthesis. These results are valuable for improving the fruit quality during development and storage.

Core cell cycle regulatory genes in rice and their expression profiles across the growth zone of the leaf

Rice (Oryza sativa L.) as a model and crop plant with a sequenced genome offers an outstanding experimental system for discovering and functionally analyzing the major cell cycle control elements in a cereal species. In this study, we identified the core cell cycle genes in the rice genome through a hidden Markov model search and multiple alignments supported with the use of short protein sequence probes. In total we present 55 rice putative cell cycle genes with locus identity, chromosomal location, approximate chromosome position and EST accession number. These cell cycle genes include nine cyclin dependent-kinase (CDK) genes, 27 cyclin genes, one CKS gene, two RBR genes, nine E2F/DP/DEL genes, six KRP genes, and one WEE gene. We also provide characteristic protein sequence signatures encoded by CDK and cyclin gene variants. Promoter analysis by the FootPrinter program discovered several motifs in the regulatory region of the core cell cycle genes. As a first step towards functional characterization we performed transcript analysis by RT-PCR to determine gene specific variation in transcript levels along the rice leaves. The meristematic zone of the leaves where cells are actively dividing was identified based on kinematic analysis and flow cytometry. As expected, expression of the majority of cell cycle genes was exclusively associated with the meristematic region. However genes such as different D-type cyclins, DEL1, KRP1/3, and RBR2 were also expressed in leaf segments representing the transition zone in which cells start differentiation.

Expression of the toxin-antitoxin genes yefM(Lrh), yoeB(Lrh) in human Lactobacillus rhamnosus isolates

Lactobacilli are important microorganisms in various activities, for example, diary products, meat ripening, bread and pickles, but, moreover, are associated directly with human skin and cavities (e.g., mouth, gut, or vagina). Some of them are used as probiotics. Therefore, the molecular biological investigation of these bacteria is important. Earlier we described several toxin antitoxin systems (type II) in lactobacilli. Here, we describe the structure and transcriptional regulation of genes, encoding TA system YefM-YoeB(Lrh) in three strains of Lactobacillus rhamnosus comparing stationary and exponential growth phases, the influence of stress factors and mRNA stability. The same TA system is responding to physiological and stress conditions differently in related strains. Using primer extension and RLM-RACE methods we determined three transcription start sites of RNAs in the operon. The promoter region of the operon is preceded by a conserved BOX element occurring at multiple positions in the genomes of L. rhamnosus strains. Downstream of and partially overlapping with the 3' end of the yoeB(Lrh) toxin gene, a divergently transcribed unexpected RNA was detected.

Proteome and transcript analysis of Vitis vinifera cell cultures subjected to Botrytis cinerea infection

Gray mold caused by Botrytis cinerea is one of the most important diseases of grapevine resulting in significant reductions in yield and fruit quality. In order to examine the molecular mechanisms that characterize the interaction between B. cinerea and the host plant, the grapevine cytoplasmic proteome was analyzed by two-dimensional polyacrylamide gel electrophoresis. The interaction between Vitis vinifera cv. Gamay cells and B. cinerea was characterized by the increase in spot abundance of 30 proteins, of which 21 were successfully identified. The majority of these proteins were related to defence and stress responses and to cell wall modifications. Some of the modulated proteins have been previously found to be affected by other pathogens when they infect V. vinifera but interestingly, the proteins related to cell wall modification that were influenced by B. cinerea have not been shown to be modulated by any other pathogen studied to date. Transcript analysis using the quantitative real time polymerase chain reaction additionally revealed the up-regulation of several acidic, probably extracellular, chitinases. The results indicate that cell wall strengthening, accumulation of PR proteins and excretion of lytic enzymes are likely to be important mechanisms in the defence of grapevine against B. cinerea.

BIOLOGICAL SIGNIFICANCE

Although gray mold caused by Botrytis cinerea is one of the most important diseases of grapevine, little information is available about proteomic changes in this pathosystem. These results suggest that cell wall strengthening, accumulation of PR proteins and excretion of lytic enzymes are important molecular mechanisms in the defence of grapevine against B. cinerea. Surprisingly, the proteins related to cell wall modification that were modulated by B. cinerea have not been shown to be affected by any other pathogen studied to date.