I am currently building a synthetic system in E.coli, and am often faced with the need to use genes from other distant prokaryotes. I know that myself and most of my colleagues resort to an educated trial and error approach. Besides the obvious (elimination of introns from eukaryotes, codon optimization, genetic relatedness), is there any predictable or semi-rational way of knowing if a transgene for a different organism will function properly in any given organism?
By looking at the sequence only? This is an unsolved problem.
Its not clear to me exactly what you are looking for, but here are some thoughts...
On a relatively narrow question as to whether any gene you plug into a bacterium, yeast, mouse, goat or other transgenic organism - the rna may not translate into protein in detectable levels or at high enough levels to get the desired result. changing the sequence of the DNA of the gene for better transcription/translation is a common necessary experimental.
On the broader systems biology level, other cofactors, substrates that are necessary for the function of the gene may have to be engineered in the host organism. That is also an open question.
All this is assuming the gene in question codes for an enzyme to make a new or different amount of the metabolic product from the host organism, a commmon synthetic biology target. If you are adding signaling pathway components, tinkering with a more specific mechanism in the cell, getting the function you desire could be a lot of work. E.g. if you were inserting a new ribosomal component or a gene related to mitosis, that would be hard to imagine a priori how it would function in the new cell or if it would just kill it.
Also, Olga Troyanskaya at Princeton CS is working on the related problem of finding the function of a gene by looking at its sequence and cross referencing to other known data. Electronic functional inference is difficult, esp when we have no complete gene functional description of any living organism to start with.