Many bacterial and archaeal promoters work backwards and forwards

C.Contrary to what is usually described in biology textbooks, transcription of bacteria and archaea in the genome can occur in opposite directions. It does this thanks to bidirectional promoters – DNA sequences that allow RNA polymerases to jump and migrate in one way or another to produce mRNA transcripts. Such promoters are not uncommon: 19 percent of all transcription start sites (TSSs) in Escherichia coli are associated with a bidirectional promoter, according to a study published May 6 in Natural microbiology.

“We were really surprised,” says study co-author Emily Warman, a postdoctoral fellow in molecular microbiology at the University of Birmingham in the UK. While previous research had described bidirectional promoters in eukaryotes as well as in some species of bacteria and archaea, the new study establishes divergent transcription – the reading of genes in both directions – as a common trait that is preserved in all three areas of life.

Bidirectional Promoters Across Biology

In eukaryotic cells, DNA wraps around histone proteins and is packaged in chromatin. Sections of DNA that are not tightly wound are accessible to RNA polymerase and other proteins required for transcription. In some cases, these regions contain two TSSs, one on each strand of DNA, oriented in opposite directions; These TSSs can be separated by hundreds or thousands of base pairs. Scientists have identified these types of bidirectional promoters in a wide variety of eukaryotic cells, from yeast to mouse macrophages.

Bacteria don’t have histones. However, some have a histone-like nucleoid structuring protein (H-NS) that binds to DNA and helps fold bacterial chromosomes. In a study published in 2014, published in Genes & Developmentresearchers found that in E. coliH-NS suppresses promoters that were taken up by horizontal gene transfer. This is the transfer of genetic material between organisms outside of reproduction. Interestingly, they found that many of the H-NS suppressed promoters were for non-coding RNAs and were in the middle of other genes.

One of Warman’s first tasks as a PhD student in David Grainger’s laboratory in Birmingham was to characterize the activity of these promoters by inserting them into a plasmid in front of a reporter gene and measuring the resulting gene expression. “A lot of the information we had about these regions didn’t tell us where the transcription was going,” she says. “To cover all of our bases, I took all of these regions and brought them in both directions.” Surprisingly, many of the promoter fragments produced activity in both orientations, meaning that the same DNA segment could direct transcription in both directions.

To find out if bidirectional promoters were common around the world E. coli Genome, the team analyzed previously obtained data sets that mapped TSSs. They found 5,292 divergent TSSs that were between 7 and 25 base pairs apart but were on different strands of DNA. These TSS pairs made up 19 percent of all TSSs in E. coli. The most common spacing between sites was 18 base pairs – much closer than the spacing observed in eukaryotic cells. This close spacing positions promoter elements, DNA sequences that are critical for the recruitment of RNA polymerase, on the two strands of DNA opposite. Therefore, the authors suggest that the RNA polymerase can attach the same stretch of DNA in two different orientations and initiate transcription in both directions.

Bidirectional promoters include two closely positioned transcription start sites (TSSs), one on each strand of DNA. These sites are upstream of gene coding regions. Researchers found that in E. coliSuch TSSs are usually separated by 18 base pairs, a distance that places promoter elements necessary for the recruitment of RNA polymerase opposite one another on the two strands of DNA.

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They examined TSSs from more types of bacteria and found that different pairs were abundant. In Proteobacteria and Actinobacteria, the TSS pairs were typically 18 or 19 base pairs apart. The team also examined previously published TSS maps for two archaic species and uncovered many different TSS pairs.

“Bidirectional transcription is also a characteristic of eukaryotic transcription, but what is important is that this paper shows that the mechanism in bacteria is different from the mechanism in eukaryotes,” says Seth Darst, a biophysicist at Rockefeller University who was absent from the study was involved The scientist by email.

In a study published in 2018, published in BMC GenomicsResearchers reported a similar finding in Pseudomonas aeruginosa, a pathogen that causes infections in humans. They found 105 TSS pairs on opposite strands, exactly 18 base pairs apart.

“We just watched Pseudomonasand we found them and found them unusual, “says Peter Unrau, biochemist at Simon Fraser University in British Columbia and co-author of the 2018 study.” They’re apparently all over the bacteria and archaea – so that’s really cool. ”

Bidirectional gene regulation

The authors suggest that bidirectional promoters could enable coordinated regulation of genes running in opposite directions. For example, transcription factors that bind a promoter region could modulate expression of two neighboring genes simultaneously. These molecular details of this and other possible forms of RNA-dependent regulation are still open questions, says Unrau.

In a study published in 2019, published in Natural microbiologyShixin Liu, biophysicist at Rockefeller University, and colleagues made a complementary discovery about transcription in E. coli: Some convergent genes that converge on each other share a bidirectional transcription terminator.

Bacteria have relatively compact genomes, says Liu. “These [bidirectional elements] seem to be a way of encoding more complex regulatory functions in their small genomes so that one promoter can control two divergent genes or one terminator can control two convergent genes at the same time. ”

The proliferation of bidirectional promoters could be remarkable for biotechnological applications where scientists want to use efficient promoters to create gene products, Warman says. “I think it’s just something that anyone interested in gene expression needs to be aware of.”

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