Reconstructing the Evolutionary History of a Highly Conserved Operon Cluster in<i>Gammaproteobacteria</i>and<i>Bacilli</i>

Brandis, Gerrit

doi:10.1093/gbe/evab041

Cited by 9 publications

(21 citation statements)

References 66 publications

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“…5 ) and SG17M ( Fig. 6 ) that were aligned from the 4-h (A) and 8-h (D) biological replicates to a gene cluster evolutionarily highly conserved in gammaproteobacteria ( 50 ). The elongation factor Tu tufB gene is flanked upstream by the triplet tRNA Tyr -tRNA Gly -tRNA Thr genes and downstream by the tRNA Trp gene, followed by the genes secE , nusG , rplK , and rplA , encoding a protein cotranslocator, a transcription termination factor, and two ribosomal proteins.…”

Section: Resultsmentioning

confidence: 99%

Direct RNA Nanopore Sequencing of Pseudomonas aeruginosa Clone C Transcriptomes

et al. 2022

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The transcriptomes of Pseudomonas aeruginosa clone C isolates NN2 and SG17M during the mid-exponential and early stationary phase of planktonic growth were evaluated by direct RNA sequencing on the nanopore platform and compared with established short-read cDNA sequencing on the Illumina platform. Fifty to ninety percent of the sense RNAs turned out to be rRNA molecules followed by similar proportions of mRNA transcripts and non-coding RNAs. Both platforms detected similar proportions of uncharged tRNAs and 29 yet undescribed antisense tRNAs. For example, the rarest arginine codon was paired with the most abundant tRNA Arg , and the tRNA Arg gene is missing for the most frequent arginine codon. More than 90% of the antisense RNA molecules were complementary to a coding sequence. The antisense RNAs were evenly distributed in the genomes. Direct RNA sequencing identified more than 4,000 distinct non-overlapping antisense RNAs during exponential and stationary growth. Besides highly expressed small antisense RNAs less than 200 bases in size, a population of longer antisense RNAs was sequenced that covered a broad range of a few hundred to thousands of bases and could be complementary to a contig of several genes. In summary, direct RNA sequencing identified yet undescribed RNA molecules and an unexpected composition of the pools of tRNAs, sense and antisense RNAs. IMPORTANCE Genome-wide gene expression of bacteria is commonly studied by high-throughput sequencing of size-selected cDNA fragment libraries of reverse-transcribed RNA preparations. However, the depletion of ribosomal RNAs, enzymatic reverse transcription and the fragmentation, size selection and amplification during library preparation lead to inevitable losses of information about the initial composition of the RNA pool. We demonstrate that direct RNA sequencing on the nanopore platform can overcome these limitations. Nanopore sequencing of total RNA yielded novel insights into the Pseudomonas aeruginosa transcriptome that – if replicated in other species – will change our view of the bacterial RNA world. The discovery of sense – antisense pairs of tmRNA, tRNAs and mRNAs indicates a further and unknown level of gene regulation in bacteria.

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Section: Resultsmentioning

confidence: 99%

Direct RNA Nanopore Sequencing of Pseudomonas aeruginosa Clone C Transcriptomes

et al. 2022

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“…We believe, to extend the scope of our model, it is necessary to understand the genetic factors essential for the insertion, deletion, and excision reactions by IS transposase and the types of ISs that promote operon formation. Future studies in such directions might also reveal the origins of ancient operons (10,19) by comparing when the genetic factors, the ISs, and the operons emerged.…”

Section: Limitations Of Our Studymentioning

confidence: 99%

“…However, the proposed model requires validation in nature. This is important as ISs are regarded as drivers of operon destruction (19,23), although this view may be biased because studies have focused more on the evolution of conserved operons than on their formation.…”

Section: Future Workmentioning

confidence: 99%

“…ISs are a major cause of genetic rearrangements (17,18) and therefore may as well facilitate operons to form. A recent study, based on the presence of ISs within ancient operons, inferred that ISs may form operons by facilitating rearrangements (19). However, no study seems to have associated the tandem deletion of surrounding genes by IS with the formation of operons.…”

Section: Introductionmentioning

confidence: 99%

“…Although ISs are known to delete neighboring sequences since at least the 1970s (20)(21)(22), deletions by IS as a mechanism that promotes the formation of operons have been undervalued for the following three main reasons: (i) IS-rich genomes seem to have more operons disrupted compared to other genomes (19,23). Therefore, ISs are often associated with the disruption rather than the formation of operons.…”

Section: Introductionmentioning

confidence: 99%

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Operon formation by insertion sequence IS3 in Escherichia coli

Kanai

Tsuru

Furusawa

2021

Preprint

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Operons are a hallmark of the genomic and regulatory architecture of prokaryotes. However, the mechanism by which two genes placed far apart gradually come close and form operons remains to be elucidated. Here, we propose a new model of the origin of operons: Mobile genetic elements called insertion sequences can facilitate the formation of operons by consecutive insertion-deletion-excision reactions. This mechanism barely leaves traces of insertion sequences and is difficult to detect in evolution in nature. We performed, to the best of our knowledge, the first experimental demonstration of operon formation, as a proof of concept. The insertion sequence IS3 and the insertion sequence excision enhancer are genes found in a broad range of bacterial species. We introduced these genes into insertion sequence-less Escherichia coli and found that, supporting our hypothesis, the activity of the two genes altered the expression of genes surrounding IS3, closed a 2.7 kilobase pair gap between a pair of genes, and formed new operons. This study shows how insertion sequences can facilitate the rapid formation of operons through locally increasing the structural mutation rates and highlights how coevolution with mobile elements may shape the organization of prokaryotic genomes and gene regulation.

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