scholarly journals A Genome-Wide Analysis of Antibiotic Producing Genes in Streptomyces globisporus SP6C4

2021 ◽  
Vol 37 (4) ◽  
pp. 389-395
Author(s):  
Da-Ran Kim ◽  
Youn-Sig Kwak
Keyword(s):  
Bacterial Species ◽  
Gene Clusters ◽  
Antimicrobial Activities ◽  
Plant Diseases ◽  
Local Alignment ◽  
Plant Tissues ◽  
Biosynthetic Gene ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Soil is the major source of plant-associated microbes. Several fungal and bacterial species live within plant tissues. Actinomycetes are well known for producing a variety of antibiotics, and they contribute to improving plant health. In our previous report, Streptomyces globisporus SP6C4 colonized plant tissues and was able to move to other tissues from the initially colonized ones. This strain has excellent antifungal and antibacterial activities and provides a suppressive effect upon various plant diseases. Here, we report the genome-wide analysis of antibiotic producing genes in S. globisporus SP6C4. A total of 15 secondary metabolite biosynthetic gene clusters were predicted using antiSMASH. We used the CRISPR/Cas9 mutagenesis system, and each biosynthetic gene was predicted via protein basic local alignment search tool (BLAST) and rapid annotation using subsystems technology (RAST) server. Three gene clusters were shown to exhibit antifungal or antibacterial activity, viz. cluster 16 (lasso peptide), cluster 17 (thiopeptide-lantipeptide), and cluster 20 (lantipeptide). The results of the current study showed that SP6C4 has a variety of antimicrobial activities, and this strain is beneficial in agriculture.

scholarly journals Energetic Evolution of Cellular Transportomes

2017 ◽  
Author(s):  
Behrooz Darbani ◽  
Douglas B. Kell ◽  
Irina Borodina
Keyword(s):  
Ion Channels ◽  
Bacterial Species ◽  
Living Cells ◽  
Energetic Efficiency ◽  
Cellular Functions ◽  
Transporter Proteins ◽  
Genome Wide Analysis ◽  
Solute Carriers ◽  
Genome Wide ◽  
A Genome

ABSTRACTTransporter proteins mediate the translocation of substances across the membranes of living cells. We performed a genome-wide analysis of the compositional reshaping of cellular transporters (the transportome) across the kingdoms of bacteria, archaea, and eukarya. We show that the transportomes of eukaryotes evolved strongly towards a higher energetic efficiency, as ATP-dependent transporters diminished and secondary transporters and ion channels proliferated. This change has likely been important in the development of tissues performing energetically costly cellular functions. The transportome analysis also indicated seven bacterial species, includingNeorickettsia risticiiandNeorickettsia sennetsu, as likely origins of the mitochondrion in eukaryotes, due to the restricted presence therein of clear homologues of modern mitochondrial solute carriers.

scholarly journals A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in a Planktothrix rubescens strain

BMC Genomics ◽  
2009 ◽  
Vol 10 (1) ◽  
pp. 396 ◽  
Author(s):  
Trine B Rounge ◽  
Thomas Rohrlack ◽  
Alexander J Nederbragt ◽  
Tom Kristensen ◽  
Kjetill S Jakobsen
Keyword(s):  
Gene Clusters ◽  
Nonribosomal Peptide Synthetase ◽  
Nonribosomal Peptide ◽  
Genome Wide Analysis ◽  
Planktothrix Rubescens ◽  
Genome Wide ◽  
A Genome ◽  
Peptide Synthetase

scholarly journals A novel fungal gene regulation system based on inducible VPR-dCas9 and nucleosome map-guided sgRNA positioning

2020 ◽  
Vol 104 (22) ◽  
pp. 9801-9822
Author(s):  
Andreas Schüller ◽  
Lisa Wolansky ◽  
Harald Berger ◽  
Lena Studt ◽  
Agnieszka Gacek-Matthews ◽  
...  
Keyword(s):  
Aspergillus Nidulans ◽  
Target Genes ◽  
Negative Impact ◽  
Constitutive Expression ◽  
Gene Clusters ◽  
Regulation System ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Genome Wide ◽  
A Genome

Abstract Programmable transcriptional regulation is a powerful tool to study gene functions. Current methods to selectively regulate target genes are mainly based on promoter exchange or on overexpressing transcriptional activators. To expand the discovery toolbox, we designed a dCas9-based RNA-guided synthetic transcription activation system for Aspergillus nidulans that uses enzymatically disabled “dead” Cas9 fused to three consecutive activation domains (VPR-dCas9). The dCas9-encoding gene is under the control of an estrogen-responsive promoter to allow induction timing and to avoid possible negative effects by strong constitutive expression of the highly active VPR domains. Especially in silent genomic regions, facultative heterochromatin and strictly positioned nucleosomes can constitute a relevant obstacle to the transcriptional machinery. To avoid this negative impact and to facilitate optimal positioning of RNA-guided VPR-dCas9 to targeted promoters, we have created a genome-wide nucleosome map from actively growing cells and stationary cultures to identify the cognate nucleosome-free regions (NFRs). Based on these maps, different single-guide RNAs (sgRNAs) were designed and tested for their targeting and activation potential. Our results demonstrate that the system can be used to regulate several genes in parallel and, depending on the VPR-dCas9 positioning, expression can be pushed to very high levels. We have used the system to turn on individual genes within two different biosynthetic gene clusters (BGCs) which are silent under normal growth conditions. This method also opens opportunities to stepwise activate individual genes in a cluster to decipher the correlated biosynthetic pathway. Keypoints • An inducible RNA-guided transcriptional regulator based on VPR-dCas9 was established in Aspergillus nidulans. • Genome-wide nucleosome positioning maps were created that facilitate sgRNA positioning. • The system was successfully applied to activate genes within two silent biosynthetic gene clusters.

scholarly journals Genome-wide Identification and Analysis of CCT Genes in Wheat (Triticum Aestivum L.)

2020 ◽  
Author(s):  
Hongwei Zhang ◽  
Xinxia Liang ◽  
Shuo Zhou ◽  
Haibo Wang
Keyword(s):  
Gene Clusters ◽  
Triticum Aestivum L ◽  
Suppressor Gene ◽  
Pcr Analysis ◽  
Genome Wide Analysis ◽  
Real Time Quantitative Pcr ◽  
Genome Wide ◽  
A Genome ◽  
Mads Box Gene ◽  
And Function

Abstract Background: The vernalization, in which the plants must undergo a prolonged winter cold exposure to flower, is mainly controlled by a suppressive MADS-box gene FLC in Arabidopsis. However, different from Arabidopsis, the CCT-domain containing gene VRN2 is the critical vernalization-related suppressor gene in cereals. Based on this apparent diversity of vernalization in different plants, and involvement of VRN2 with vernalization in cereals, we conducted a genome-wide analysis of CCT genes in wheat, and the relationship between vernalization and these genes were also revealed.Results: A genome-wide analysis of the CCT genes in common wheat was performed by employing a hidden Markov model-based method, and 127 sequences, which assigned to 40 clusters, were obtained in three subgenomes. Specially, two of the gene clusters are duplicated, and distinguishingly located near telomere. Furthermore, these sequences were classified into eight groups by a phylogenetic analysis procedure using the UPGMA method, and this taxonomy is concordant to the classification based on CCT interruptions and domain organization which roughly divided the proteins into four divergently related subfamilies. Moreover, the expression of several CCT genes is continually downregulated during and after vernalization, but no continually upregulated CCT genes were revealed, as indicated by transcriptome sequencing and real-time quantitative PCR analysis.Conclusion: This study improves our understanding of the structure and function of CCT genes, suggests many vernalization-related CCT genes, and may guide future investigations on CCT genes and vernalization in wheat.

scholarly journals A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2 in chromosome end protection

2008 ◽  
Vol 9 (10) ◽  
pp. R146 ◽  
Author(s):  
Amanda Greenall ◽  
Guiyuan Lei ◽  
Daniel C Swan ◽  
Katherine James ◽  
Liming Wang ◽  
...  
Keyword(s):  
Budding Yeast ◽  
Biosynthetic Gene ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Chromosome End Protection

scholarly journals CRISPR-based transcriptional activation tool for silent genes in filamentous fungi

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
László Mózsik ◽  
Mirthe Hoekzema ◽  
Niels A. W. de Kok ◽  
Roel A. L. Bovenberg ◽  
Yvonne Nygård ◽  
...  
Keyword(s):  
Filamentous Fungi ◽  
Transcriptional Activation ◽  
Core Promoter ◽  
Crop Protection ◽  
Gene Clusters ◽  
Growth Conditions ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Fluorescent Reporter ◽  
A Genome

AbstractFilamentous fungi are historically known to be a rich reservoir of bioactive compounds that are applied in a myriad of fields ranging from crop protection to medicine. The surge of genomic data available shows that fungi remain an excellent source for new pharmaceuticals. However, most of the responsible biosynthetic gene clusters are transcriptionally silent under laboratory growth conditions. Therefore, generic strategies for activation of these clusters are required. Here, we present a genome-editing-free, transcriptional regulation tool for filamentous fungi, based on the CRISPR activation (CRISPRa) methodology. Herein, a nuclease-defective mutant of Cas9 (dCas9) was fused to a highly active tripartite activator VP64-p65-Rta (VPR) to allow for sgRNA directed targeted gene regulation. dCas9-VPR was introduced, together with an easy to use sgRNA “plug-and-play” module, into a non-integrative AMA1-vector, which is compatible with several filamentous fungal species. To demonstrate its potential, this vector was used to transcriptionally activate a fluorescent reporter gene under the control of the penDE core promoter in Penicillium rubens. Subsequently, we activated the transcriptionally silent, native P. rubens macrophorin biosynthetic gene cluster by targeting dCas9-VPR to the promoter region of the transcription factor macR. This resulted in the production of antimicrobial macrophorins. This CRISPRa technology can be used for the rapid and convenient activation of silent fungal biosynthetic gene clusters, and thereby aid in the identification of novel compounds such as antimicrobials.

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