Forward or Reverse Strand: Is there a difference when encoding genetic devices?

Question

Background:

In synthetic biology, and also in nature, there are lots of examples of genes in both the forward and reverse orientation. It seems in synthetic biology/bioengineering, most genetic devices are, by default, encoded on the forward strand unless there are concerns of readthrough from one expression unit to another, in which case one of the expression units is included on the reverse strand like below:

It also seems that genes are sometimes in the reverse orientation for no apparent reason, especially in plasmid backbones:

The Question:

My question is, ignoring issues of potential readthrough, does it matter which strand a genetic device is encoded on? So in the example below, would there be any difference between A and B, or does it not matter? Also, does whether it's on a plasmid compared to a genome matter? I'm specifically interested in bacteria here.

This seems like it should be a simple question to answer and I'm sure I'm just missing something, but I can't find anything about it.

Answer 1

First, I think you have misunderstood the concept of sense/antisense. These are defined individually for each gene, with the sense strand always referring to the coding (non-template) strand of a gene, and the antisense strand to its complement, the non-coding (template) strand. So in your plasmid example above, all genes are encoded by their respective sense strand, but which of the two strands that is sense for a given gene depends on its orientation. There is therefore no biologically meaningful sense/antisense concept for entire genomes, chromosomes or plasmids. Read more in the Wikipedia article on sense, and the answers to this SE Biology question.

Having said that, it should be clear that the expression cassettes pictured in figues A) and B) are completely identical. If you ignore the context around them (e.g. readthrough), their direction is irrelevant.

It also seems that genes are sometimes encoded on the reverse strand for no apparent reason, especially in plasmid backbones

Many commonly used plasmid backbones derive from vectors that date many decades back, to a time when cloning strategies were far from as flexible as today. Researchers were generally limited by the restriction sites occurring naturally in the DNA sequences. A gene's position and orientation with respect to its neighbouring genes might therefore be the simple result of lack of other cloning options - although I honestly doubt "wrong" orientation would even have been considered an issue. For an example you could read about plasmid pBR322 in this Wikipedia article, and references therein.