scholarly journals Transcriptome Analysis Unveils the Effects of Proline on Gene Expression in the Yeast Komagataella phaffii

2021 ◽  
Vol 10 (1) ◽  
pp. 67
Author(s):  
Andrey Rumyantsev ◽  
Anton Sidorin ◽  
Artemii Volkov ◽  
Ousama Al Shanaa ◽  
Elena Sambuk ◽  
...  

Komagataella phaffii yeast is one of the most important biocompounds producing microorganisms in modern biotechnology. Optimization of media recipes and cultivation strategies is key to successful synthesis of recombinant proteins. The complex effects of proline on gene expression in the yeast K. phaffii was analyzed on the transcriptome level in this work. Our analysis revealed drastic changes in gene expression when K. phaffii was grown in proline-containing media in comparison to ammonium sulphate-containing media. Around 18.9% of all protein-encoding genes were differentially expressed in the experimental conditions. Proline is catabolized by K. phaffii even in the presence of other nitrogen, carbon and energy sources. This results in the repression of genes involved in the utilization of other element sources, namely methanol. We also found that the repression of AOX1 gene promoter with proline can be partially reversed by the deletion of the KpPUT4.2 gene.

2018 ◽  
Author(s):  
Viesta Beby Fadlitha ◽  
Fuki Yamamoto ◽  
Irfan Idris ◽  
Haslindah Dahlan ◽  
Naoya Sato ◽  
...  

AbstractLeprosy is a chronic infection where the skin and peripheral nervous system is invaded byMycobacterium leprae. The infection mechanism remains unknown in part because culture methods have not been established yet forM.leprae.Mce1A protein (442 aa) is coded by mce1A (1326 bp) ofM.leprae. The mce1A homolog inMycobacterium tuberculosisis known to be associated withM.tuberculosisepithelial cell entry, and survival and multiplication within macrophages. Studies using recombinant proteins have indicated that mce1A ofM.lepraeis also associated with epithelial cell entry. This study is aimed at identifying particular sequences within mce1A associated withM.lepraeepithelial cell entry.Recombinant proteins having N-terminus and C-terminus truncations of the mce1A region ofM.lepraewere created inEschericia coli.Entry activity of latex beads, coated with these truncated proteins (r-lep37kDa and r-lep27kDa), into HeLa cells was observed by electron microscopy. The entry activity was preserved even when 315 bp (105 aa) and 922 bp (308 aa) was truncated from the N-terminus and C-terminus, respectively. This 316 – 921 bp region was divided into three sub-regions: 316 – 531 bp (InvX), 532 – 753 bp (InvY), and 754 – 921 bp (InvZ). Each sub-region was cloned into an AIDA vector and expressed on the surface ofE.coli.Entry of theseE.coliinto monolayer-cultured HeLa and RPMI2650 cells was observed by electron microscopy. OnlyE.coliharboring the InvX sub-region exhibited cell entry. InvX was further divided into 4 domains, InvXa - InvXd, containing sequences 1 – 24 aa, 25 – 46 aa, 47 – 57 aa, and 58 – 72 aa, respectively.RecombinantE.coli, expressing each of InvXa - InvXd on the surface, were treated with antibodies against these domains, then added to monolayer cultured RPMI cells. The effectiveness of these antibodies in preventing cell entry was studied by colony counting. Entry activity was suppressed by antibodies against InvXa, InvXb, and InvXd. This suggests that these three InvX domains of mce1A are important forM.lepraeinvasion into nasal epithelial cells.Author SummaryMce1A protein is encoded by the mce1A region of mce1 locus ofM.tuberculosisandM.leprae, and is involved in the bacteria’s invasion into epithelial cells. The present study revealed that the active sequence ofM.lepraeinvolved in the invasion into nasal mucosa epithelial cells is present in the 316-531 bp region of mce1A.The most important region of mce1A protein involved in the invasion ofM.tuberculosisinto human epithelial cells is called the InvIII region, which is located between amino acids at position 130 to 152. The InvIII region ofM.tuberculosiscorresponds to InvXb ofM.leprae. The sequences of these regions are identical between amino acids at positions 10 to position 22 as counted from the N terminus, except that amino acids at positions 1 to 3, 5, 8, 9, 13 are different betweenM.lepraeandM.tuberculosis. Suppression test results also indicated that the most important region of mce1A protein ofM.lepraeinvolved in the invasion into human epithelial cells is different from thatM.tuberculosis. WhileM.tuberculosishas 3,959 protein-encoding genes and only 6 pseudogenes,M.lepraehas only 1,604 protein-encoding genes but has 1,116 pseudogenes indicating that inM.leprae, far more proteins are inactivated as compared toM.tuberculosis. The present study also revealed that, as inM.tuberculosis,the mce1A protein is expressed on the surface of bacteria as a native protein. In light of these data, the mce1A protein is considered to be one of the most important proteins involved in the invasion ofM.lepraeinto nasal mucosa epithelial cells.


2015 ◽  
Vol 119 (4) ◽  
pp. 321-327 ◽  
Author(s):  
Tyler J. Kirby ◽  
Jonah D. Lee ◽  
Jonathan H. England ◽  
Thomas Chaillou ◽  
Karyn A. Esser ◽  
...  

The ability of skeletal muscle to hypertrophy in response to a growth stimulus is known to be compromised in older individuals. We hypothesized that a change in the expression of protein-encoding genes in response to a hypertrophic stimulus contributes to the blunted hypertrophy observed with aging. To test this hypothesis, we determined gene expression by microarray analysis of plantaris muscle from 5- and 25-mo-old mice subjected to 1, 3, 5, 7, 10, and 14 days of synergist ablation to induce hypertrophy. Overall, 1,607 genes were identified as being differentially expressed across the time course between young and old groups; however, the difference in gene expression was modest, with cluster analysis showing a similar pattern of expression between the two groups. Despite ribosome protein gene expression being higher in the aged group, ribosome biogenesis was significantly blunted in the skeletal muscle of aged mice compared with mice young in response to the hypertrophic stimulus (50% vs. 2.5-fold, respectively). The failure to upregulate pre-47S ribosomal RNA (rRNA) expression in muscle undergoing hypertrophy of old mice indicated that rDNA transcription by RNA polymerase I was impaired. Contrary to our hypothesis, the findings of the study suggest that impaired ribosome biogenesis was a primary factor underlying the blunted hypertrophic response observed in skeletal muscle of old mice rather than dramatic differences in the expression of protein-encoding genes. The diminished increase in total RNA, pre-47S rRNA, and 28S rRNA expression in aged muscle suggest that the primary dysfunction in ribosome biogenesis occurs at the level of rRNA transcription and processing.


2015 ◽  
Vol 14s1 ◽  
pp. CIN.S13972 ◽  
Author(s):  
Qian Wu ◽  
Kyoung-Jae Won ◽  
Hongzhe Li

Chromatin immunoprecipitation sequencing (ChIP-seq) is a powerful method for analyzing protein interactions with DNA. It can be applied to identify the binding sites of transcription factors (TFs) and genomic landscape of histone modification marks (HMs). Previous research has largely focused on developing peak-calling procedures to detect the binding sites for TFs. However, these procedures may fail when applied to ChIP-seq data of HMs, which have diffuse signals and multiple local peaks. In addition, it is important to identify genes with differential histone enrichment regions between two experimental conditions, such as different cellular states or different time points. Parametric methods based on Poisson/negative binomial distribution have been proposed to address this differential enrichment problem and most of these methods require biological replications. However, many ChIP-seq data usually have a few or even no replicates. We propose a nonparametric method to identify the genes with differential histone enrichment regions even without replicates. Our method is based on nonparametric hypothesis testing and kernel smoothing in order to capture the spatial differences in histone-enriched profiles. We demonstrate the method using ChIP-seq data on a comparative epigenomic profiling of adipogenesis of murine adipose stromal cells and the Encyclopedia of DNA Elements (ENCODE) ChIP-seq data. Our method identifies many genes with differential H3K27ac histone enrichment profiles at gene promoter regions between proliferating preadipocytes and mature adipocytes in murine 3T3-L1 cells. The test statistics also correlate with the gene expression changes well and are predictive to gene expression changes, indicating that the identified differentially enriched regions are indeed biologically meaningful.


2003 ◽  
Vol 185 (19) ◽  
pp. 5854-5861 ◽  
Author(s):  
Olena Perlova ◽  
Alejandro Ureta ◽  
Stefan Nordlund ◽  
Dietmar Meletzus

ABSTRACT In our studies on the regulation of nitrogen metabolism in Gluconacetobacter diazotrophicus, an endophytic diazotroph of sugarcane, three glnB-like genes were identified and their role(s) in the control of nitrogen fixation was studied. Sequence analysis revealed that one PII protein-encoding gene, glnB, was adjacent to a glnA gene (encoding glutamine synthetase) and that two other PII protein-encoding genes, identified as glnK1 and glnK2, were located upstream of amtB1 and amtB2, respectively, genes which in other organisms encode ammonium (or methylammonium) transporters. Single and double mutants and a triple mutant with respect to the three PII protein-encoding genes were constructed, and the effects of the mutations on nitrogenase expression and activity in the presence of either ammonium starvation or ammonium sufficiency were studied. Based on the results presented here, it is suggested that none of the three PII homologs is required for nif gene expression, that the GlnK2 protein acts primarily as an inhibitor of nif gene expression, and that GlnB and GlnK1 control the expression of nif genes in response to ammonium availability, both directly and by relieving the inhibition by GlnK2. This model includes novel regulatory features of PII proteins.


Author(s):  
И.В. Пронина ◽  
Е.А. Филиппова ◽  
С.С. Лукина ◽  
А.М. Бурденный ◽  
Т.П. Казубская ◽  
...  

Рак молочной железы (РМЖ) характеризуется эпигенетическими нарушениями, которые приводят к нарушению регуляции экспрессии опухоль ассоциированных белок-кодирующих генов, что влияет на развитие опухоли. Цель исследования - поиск новых микроРНК, потенциально вовлеченных в регуляцию экспрессии 3 белок-кодирующих генов (AXL, DAPK1, NFIB), связанных с регуляцией апоптоза и эпителиально-мезенхимального перехода при РМЖ. Методом количественной ПЦР определены изменения экспрессии 3 белок-кодирующих генов (AXL, DAPK1, NFIB) и 3 микроРНК (miR-127-5p, -132-3р, -9-5p), предсказанных с помощью алгоритмов miRWalk 2.0 как регуляторные. Определены статистически значимые отрицательные корреляции между изменениями уровней экспрессии микроРНК и мРНК для следующих пар: miR-127-5p - DAPK1 (Rs = -0,503, p = 0,001) и miR-9-5p - DAPK1 (Rs = -0,335, p = 0,040). Таким образом, установлена потенциальная роль двух микроРНК в регуляции экспрессии гена DAPK1, активатора различных путей апоптоза и негативного регулятора ЭМП, что имеет фундаментальное значение и может найти применение для разработки таргетной терапии РМЖ. Breast cancer (BC) is characterized by epigenetic disorders, which lead to dysregulation of protein-coding gene expression; together these result in development of a tumor. The goal of the study was to search for new miRNAs that are potentially involved in regulation of the expression of three protein-encoding genes (AXL, DAPK1, NFIB) associated with regulation of apoptosis and the epithelial-mesenchymal transition in breast cancer. Quantitative PCR was used to determine changes in the expression of three protein-coding genes (AXL, DAPK1, NFIB) and three miRNAs (miR-127-5p, -132-3p, -9-5p) that had been predicted to be regulators by miRWalk 2.0 algorithms. Statistically significant negative correlations between changes in miRNA and mRNA expression were determined for the following pairs: miR-127-5p - DAPK1 (Rs = -0.503, p = 0.001) and miR-9-5p - DAPK1 (Rs = -0.335, p = 0.040). Therefore, the study showed a potential role of two miRNAs in regulation of the DAPK1 gene expression, an activator of various apoptotic pathways and a negative regulator of EMT. This result is fundamentally important and can be used to develop targeted therapies for breast cancer.


2020 ◽  
Vol 6 (10) ◽  
Author(s):  
Domenico Giosa ◽  
Maria Rosa Felice ◽  
Letterio Giuffrè ◽  
Riccardo Aiese Cigliano ◽  
Andreu Paytuví-Gallart ◽  
...  

Sporothrix schenckii is a dimorphic fungus existing as mould in the environment and as yeast in the host. The morphological shift between mycelial/yeast phases is crucial for its virulence, but the transcriptional networks implicated in dimorphic transition are still not fully understood. Here, we report the global transcriptomic differences occurring between mould and yeast phases of S. schenckii, including changes in gene expression profiles associated with these distinct cellular phenotypes. Moreover, we also propose a new genome annotation, which reveals a more complex transcriptional architecture than previously assumed. Using RNA-seq, we identified a total of 17 307 genes, of which 11 217 were classified as protein-encoding genes, whereas 6090 were designated as non-coding RNAs (ncRNAs). Approximately ~71 % of all annotated genes were found to overlap and the different-strand overlapping type was the most common. Gene expression analysis revealed that 8795 genes were differentially regulated among yeast and mould forms. Differential gene expression was also observed for antisense ncRNAs overlapping neighbouring protein-encoding genes. The release of transcriptome-wide data and the establishment of the Sporothrix Genome DataBase (http://sporothrixgenomedatabase.unime.it) represent an important milestone for Sporothrix research, because they provide a strong basis for future studies on the molecular pathways involved in numerous biological processes.


2001 ◽  
Vol 183 (5) ◽  
pp. 1688-1693 ◽  
Author(s):  
Kelly A. Bidle ◽  
Douglas H. Bartlett

ABSTRACT We are currently investigating the role of ToxR-mediated gene regulation in Photobacterium profundum strain SS9. SS9 is a moderately piezophilic (“pressure loving”) psychrotolerant marine bacterium belonging to the family Vibrionaceae. InVibrio cholerae, ToxR is a transmembrane DNA binding protein involved in mediating virulence gene expression in response to various environmental signals. A homolog to V. choleraeToxR that is necessary for pressure-responsive gene expression of two outer membrane protein-encoding genes was previously found in SS9. To search for additional genes regulated by ToxR in SS9, we have used RNA arbitrarily primed PCR (RAP-PCR) with wild-type and toxRmutant strains of SS9. Seven ToxR-activated transcripts and one ToxR-repressed transcript were identified in this analysis. The cDNAs corresponding to these partial transcripts were cloned and sequenced, and ToxR regulation of their genes was verified. The products of these genes are all predicted to fall into one or both of two functional categories, those whose products alter membrane structure and/or those that are part of a starvation response. The transcript levels of all eight newly identified genes were also characterized as a function of hydrostatic pressure. Various patterns of pressure regulation were observed, indicating that ToxR activation or repression cannot be used to predict the influence of pressure on gene expression in SS9. These results provide further information on the nature of the ToxR regulon in SS9 and indicate that RAP-PCR is a useful approach for the discovery of new genes under the control of global regulatory transcription factors.


2006 ◽  
Vol 188 (3) ◽  
pp. 1120-1133 ◽  
Author(s):  
Fionnuala McAleese ◽  
Shang Wei Wu ◽  
Krzysztof Sieradzki ◽  
Paul Dunman ◽  
Ellen Murphy ◽  
...  

ABSTRACT Custom-designed gene chips (Affymetrix) were used to determine genetic relatedness and gene expression profiles in Staphylococcus aureus isolates with increasing MICs of vancomycin that were recovered over a period of several weeks from the blood and heart valve of a patient undergoing extensive vancomycin therapy. The isolates were found to be isogenic as determined by the GeneChip based genotyping approach and thus represented a unique opportunity to study changes in gene expression that may contribute to the vancomycin resistance phenotype. No differences in gene expression were detected between the parent strain, JH1, and JH15, isolated from the nares of a patient contact. Few expression changes were observed between blood and heart valve isolates with identical vancomycin MICs. A large number of genes had altered expression in the late stage JH9 isolate (MIC = 8 μg/ml) compared to JH1 (MIC = 1 μg/ml). Most genes with altered expression were involved in housekeeping functions or cell wall biosynthesis and regulation. The sortase-encoding genes, srtA and srtB, as well as several surface protein-encoding genes were downregulated in JH9. Two hypothetical protein-encoding genes, SAS016 and SA2343, were dramatically overexpressed in JH9. Interestingly, 27 of the genes with altered expression in JH9 grown in drug-free medium were found to be also overexpressed when the parental strain JH1 was briefly exposed to inhibitory concentrations of vancomycin, and more than half (17 of 27) of the genes with altered expression belonged to determinants that were proposed to form part of a general cell wall stress stimulon (S. Utaida et al., Microbiology 149:2719-2732, 2003).


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kim Hoa Ho ◽  
Annarita Patrizi

AbstractChoroid plexus (ChP), a vascularized secretory epithelium located in all brain ventricles, plays critical roles in development, homeostasis and brain repair. Reverse transcription quantitative real-time PCR (RT-qPCR) is a popular and useful technique for measuring gene expression changes and also widely used in ChP studies. However, the reliability of RT-qPCR data is strongly dependent on the choice of reference genes, which are supposed to be stable across all samples. In this study, we validated the expression of 12 well established housekeeping genes in ChP in 2 independent experimental paradigms by using popular stability testing algorithms: BestKeeper, DeltaCq, geNorm and NormFinder. Rer1 and Rpl13a were identified as the most stable genes throughout mouse ChP development, while Hprt1 and Rpl27 were the most stable genes across conditions in a mouse sensory deprivation experiment. In addition, Rpl13a, Rpl27 and Tbp were mutually among the top five most stable genes in both experiments. Normalisation of Ttr and Otx2 expression levels using different housekeeping gene combinations demonstrated the profound effect of reference gene choice on target gene expression. Our study emphasized the importance of validating and selecting stable housekeeping genes under specific experimental conditions.


Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1272
Author(s):  
Judit Tajti ◽  
Magda Pál ◽  
Tibor Janda

Oat (Avena sativa L.) is a widely cultivated cereal with high nutritional value and it is grown mainly in temperate regions. The number of studies dealing with gene expression changes in oat continues to increase, and to obtain reliable RT-qPCR results it is essential to establish and use reference genes with the least possible influence caused by experimental conditions. However, no detailed study has been conducted on reference genes in different tissues of oat under diverse abiotic stress conditions. In our work, nine candidate reference genes (ACT, TUB, CYP, GAPD, UBC, EF1, TBP, ADPR, PGD) were chosen and analysed by four statistical methods (GeNorm, Normfinder, BestKeeper, RefFinder). Samples were taken from two tissues (leaves and roots) of 13-day-old oat plants exposed to five abiotic stresses (drought, salt, heavy metal, low and high temperatures). ADPR was the top-rated reference gene for all samples, while different genes proved to be the most stable depending on tissue type and treatment combinations. TUB and EF1 were most affected by the treatments in general. Validation of reference genes was carried out by PAL expression analysis, which further confirmed their reliability. These results can contribute to reliable gene expression studies for future research in cultivated oat.


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