Zayed et al. (2022) "Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome"; expressed sequences or transcribed?

Question

Phys.org's Ocean water samples yield treasure trove of RNA virus data summarizes Zayed et al. (April 7, 2022) in Science Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome.

The Phys.org summary includes the following paragraph:

In these current efforts to detect RNA viruses, there were no viral particles to study. Instead, researchers extracted sequences from genes expressed in organisms floating in the sea, and narrowed the analysis to RNA sequences that contained a signature gene, called RdRp, which has evolved for billions of years in RNA viruses, and is absent from other viruses or cells.

When I hear expression I think of a polypeptide final product, although it is certainly a multistep process. My understanding is that the data analyzed by Zayed et al. were RNA sequences extracted from the seawater, and not protein.

I'm thinking that "transcribed" or perhaps just "present" should have been used (depending on the details of the methodology) instead of "expressed" but I'm not sure of that at all. Wikipedia's Orthornavirae describes the transcription so I know that one does not have to start with DNA to invoke the term transcription:

The RdRp is used to transcribe the viral RNA genome into messenger RNA (mRNA) and to replicate the genome

This is the extent of my understanding here, so I'd like to ask:

Question: In Zayed et al. (2022) "Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome" did the study look at "expressed" sequences, or "transcribed", or both, or neither?

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Related:

• In marine DNA viral diversity studies, what would "paradigm of rampant mosaicism" refer to? (2019)

Answer 1

Pardon me for not specifically answering with regard to marine viruses; I think the crux of an answer depends on addressing your misconception!

expressed sequences or transcribed?

This is semantics, and important semantics to be familiarized with in biology research.

The word expression is not the most strictly defined word, and is used differently and in a context-dependent fashion. For example, in such research as you point to, one often studies gene expression by looking at the transcriptome independently, to "gauge which genes are expressed", without assurance of translation of said RNA into protein, nor assurance of localization, or function, or even maintenance of said protein. The life history of every protein certainly goes beyond the central dogma of molecular biology, and many simplify the picture into only gene transcription and translation, but these are just proxies (or rather stages) of gene expression. Translation itself is no guarantee of final function (i.e. points or stages at which it may be easy to quantitatively measure expression, which can only be indicative).

Expression is most often associated with the process of active use of a gene, of it being 'put into play'. This is unfortunately complicated by the fact that being 'put into play' requires passage through a lot of hoops. It is NOT synonymous with transcription, or a gene that crosses the transcription + translation hurdle.

Real life use

Colloquially, you can say a gene will be expressed when a signal reaches the nucleus that will put a cascade of transcription factors into motion that will eventually assemble transcriptional machinery to transcribe a gene. Hormones can 'cause' gene expression. Alternatively, you can say expression can occur when ribosomes are unblocked or assembled, or post-transcriptional silencing machinery is lifted to re-allow translation of specific mRNA strands. Yet further, a gene is clearly not 'expressed' if the protein is non-existent, and this can come about through improper folding or swift removal or mislocalization, and so on. There are many contexts in which you can use this flexible word, and it always has a connotation of gene information flow, rather than a mechanism which is responsible for gene information flow. Today, the word expression is often used more frequently on the transcriptional side of things, where we have an easier time using robust and longer-established techniques (e.g. RNA-seq) and talking about results than on the protein translational side of things, which require further insights into post-translational modifications, trafficking, integration into membranes, protein folding chemistry, export, all that jazz. However, do not forget that proper insulin gene expression really ultimately means that the resultant protein-hormone insulin is in active circulation in the body... and NOT that insulin-coding mRNAs are present abundantly in the cytoplasm of beta cells of the pancreas.

Take-home lesson: remember, the central dogma (DNA->RNA->protein) is an organizing concept, and many words refer to it, but these same words may not be comprehensive or technical or stringent enough to describe particular events, only our conceptualization of them.

tl;dr

Transcription is a specific term (copy-reading of DNA into mRNA strands) while expression is a conceptual term (which points to but does not completely encompass information flow from DNA into protein, eventually)