The global transcriptional landscape of Bacillus amyloliquefaciens XH7 and high-throughput screening of strong promoters based on RNA-seq data

Liao, Yuling; Huang, Lianggang; Wang, Bin; Zhou, Feng; Pan, Li

doi:10.1016/j.gene.2015.06.066

Cited by 33 publications

(15 citation statements)

References 54 publications

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“…Studies in most bacteria have typically reported only a few leaderless mRNAs as, for example, 12 leaderless genes in L. pneumophila (Sahr et al, 2012), 20 in Helicobacter pylori (Bischler et al, 2015), 23 in Salmonella typhimurium (Kröger et al, 2012), 30–41 in Prochlorococcus spp. (Voigt et al, 2014), and 57 in Bacillus amyloliquefaciens (Liao et al, 2015). However, an abundance of leaderless transcripts have recently been identified in the genomes of Deinococus deserti (1174 leaderless mRNAs) (de Groot et al, 2014), and M. tuberculosis (505 leaderless mRNAs) (Cortes et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans

Zhukova

Fernandes

Hugon

et al. 2017

Front. Cell. Infect. Microbiol.

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Leptospira are emerging zoonotic pathogens transmitted from animals to humans typically through contaminated environmental sources of water and soil. Regulatory pathways of pathogenic Leptospira spp. underlying the adaptive response to different hosts and environmental conditions remains elusive. In this study, we provide the first global Transcriptional Start Site (TSS) map of a Leptospira species. RNA was obtained from the pathogen Leptospira interrogans grown at 30°C (optimal in vitro temperature) and 37°C (host temperature) and selectively enriched for 5′ ends of native transcripts. A total of 2865 and 2866 primary TSS (pTSS) were predicted in the genome of L. interrogans at 30 and 37°C, respectively. The majority of the pTSSs were located between 0 and 10 nucleotides from the translational start site, suggesting that leaderless transcripts are a common feature of the leptospiral translational landscape. Comparative differential RNA-sequencing (dRNA-seq) analysis revealed conservation of most pTSS at 30 and 37°C. Promoter prediction algorithms allow the identification of the binding sites of the alternative sigma factor sigma 54. However, other motifs were not identified indicating that Leptospira consensus promoter sequences are inherently different from the Escherichia coli model. RNA sequencing also identified 277 and 226 putative small regulatory RNAs (sRNAs) at 30 and 37°C, respectively, including eight validated sRNAs by Northern blots. These results provide the first global view of TSS and the repertoire of sRNAs in L. interrogans. These data will establish a foundation for future experimental work on gene regulation under various environmental conditions including those in the host.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans

Zhukova

Fernandes

Hugon

et al. 2017

Front. Cell. Infect. Microbiol.

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“…Although transcription is the first and key step in the process of gene expression [12], the transcriptional effectiveness of one promoter varies for different proteins, and the so-called optimal promoter sequences cannot be generalized for all heterologous enzymes [13,14]. Consequently, some researchers have considered the compatibility between expression elements and the host for the production of enzymes, and have intensively investigated the endogenous expression elements, combining suitable expression patterns to reduce host-intrinsic expression bottlenecks and thereby improve protein production [15][16][17]. It is well known that effective gene expression patterns play a pivotal role in the progression from the lab bench toward industrial applications.…”

Section: Introductionmentioning

confidence: 99%

Optimized expression and enhanced production of alkaline protease by genetically modified Bacillus licheniformis 2709

Zhou

et al. 2020

Microb Cell Fact

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Background: Bacillus licheniformis 2709 is extensively applied as a host for the high-level production of heterologous proteins, but Bacillus cells often possess unfavorable wild-type properties, such as production of viscous materials and foam during fermentation, which seriously influenced the application in industrial fermentation. How to develop it from a soil bacterium to a super-secreting cell factory harboring less undomesticated properties always plays vital role in industrial production. Besides, the optimal expression pattern of the inducible enzymes like alkaline protease has not been optimized by comparing the transcriptional efficiency of different plasmids and genomic integration sites in B. licheniformis. Result: Bacillus licheniformis 2709 was genetically modified by disrupting the native lchAC genes related to foaming and the eps cluster encoding the extracellular mucopolysaccharide via a markerless genome-editing method. We further optimized the expression of the alkaline protease gene (aprE) by screening the most efficient expression system among different modular plasmids and genomic loci. The results indicated that genomic expression of aprE was superior to plasmid expression and finally the transcriptional level of aprE greatly increased 1.67-fold through host optimization and chromosomal integration in the vicinity of the origin of replication, while the enzyme activity significantly improved 62.19% compared with the wild-type alkaline protease-producing strain B. licheniformis. Conclusion: We successfully engineered an AprE high-yielding strain free of undesirable properties and its fermentation traits could be applied to bulk-production by host genetic modification and expression optimization. In summary, host optimization is an enabling technology for improving enzyme production by eliminating the harmful traits of the host and optimizing expression patterns. We believe that these strategies can be applied to improve heterologous protein expression in other Bacillus species.

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“…In prokaryotic genomes, the typical RNA-seq could be applied to: (1) uncover the global transcriptional profile in genome scale, identify differentially expressed genes (DEGs) and determine the differences in transcriptional levels between wild type and its mutants at distinct conditions (Wang et al, 2013b ; Li et al, 2016 ; Hendrickson et al, 2017 ); (2) identify 5′-ends of transcript (Wang et al, 2013a ; Liao et al, 2015 ); single-nucleotide resolution enables RNA-seq to globally identify the first nucleotide in 5′-ends. Previously, 5′-ends of transcript were generally identified by 5′-Rapid Amplification of cDNA Ends (5′-RACE), which is troublesome and costly; (3) correct gene structural annotation (Perkins et al, 2009 ); currently, the majority of sequenced bacterial genomes are annotated by an algorithm-based program which is automated but error-prone.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Landscape of Mycobacterium smegmatis

Li¹,

Han²,

Chen³

et al. 2017

Front. Microbiol.

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The non-pathogenic bacterium Mycobacterium smegmatis mc2155 has been widely used as a model organism in mycobacterial research, yet a detailed study about its transcription landscape remains to be established. Here we report the transcriptome, expression profiles and transcriptional structures through growth-phase-dependent RNA sequencing (RNA-seq) as well as other related experiments. We found: (1) 2,139 transcriptional start sites (TSSs) in the genome-wide scale, of which eight samples were randomly selected and further verified by 5′-RACE; (2) 2,233 independent monocistronic or polycistronic mRNAs in the transcriptome within the operon/sub-operon structures which are classified into five groups; (3) 47.50% (1016/2139) genes were transcribed into leaderless mRNAs, with the TSSs of 41.3% (883/2139) mRNAs overlapping with the first base of the annotated start codon. Initial amino acids of MSMEG_4921 and MSMEG_6422 proteins were identified by Edman degradation, indicating the presence of distinctive widespread leaderless features in M. smegmatis mc2155. (4) 150 genes with potentially wrong structural annotation, of which 124 proposed genes have been corrected; (5) eight highly active promoters, with their activities further determined by β-galactosidase assays. These data integrated the transcriptional landscape to genome information of model organism mc2155 and lay a solid foundation for further works in Mycobacterium.

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The global transcriptional landscape of Bacillus amyloliquefaciens XH7 and high-throughput screening of strong promoters based on RNA-seq data

Cited by 33 publications

References 54 publications

Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans

Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans

Optimized expression and enhanced production of alkaline protease by genetically modified Bacillus licheniformis 2709

Transcriptome Landscape of Mycobacterium smegmatis

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