Recently, progress in genetic engineering has increased the scale of projects that are achievable

Recently, progress in genetic engineering has increased the scale of projects that are achievable. manipulating gene clusters will move towards an era of genome engineering, where multiple functions can be mixed-and-matched to create a designer organism. Keywords:Systems Biology, Genetic Parts, Devices, Refactoring, Biotechnology == Introduction == Gene clusters are the genetic building blocks of bacteria and archaea. Prokaryotic genomes are highly organized and the genes associated with a particular function often occur near each other [1]. Occasionally, all of the genes that are necessary for a discrete function form a cluster in the genome. These clusters encode functions that affect all aspects of the life style of bacteria, including nutrient scavenging, energy production, chemical synthesis, and environmental sensing. Large protein scaffolds, nano-machines, and cytoplasmic organelles are also encoded within clusters. These functions could play a central role for many applications in biotechnology; however, their complexity makes them difficult to engineer. Here, we survey the wide range of cellular functions that are known to be encoded in these genetically compact units with an eye on their potential ability to be transferable modules in multiple host species for engineering applications. The organization of genes into clusters may facilitate the transfer of complete functions during evolution [1,2]. All of the Phensuximide gene clusters presented in this review have some evidence for horizontal transfer, including phylogenetic trees disparate from ribosomal RNA, differing G+C content, and the presence of flanking transposon/integron genes [3,4]. Phage genomes and Mouse monoclonal to PTK6 conjugative plasmids also contain bacterial gene clusters, implying that a mobile element can confer a fitness advantage on its host by adding a novel function. For example, the photosynthetic apparatus [5] and type IV pili [6] have been observed in phage genomes. Because gene clusters appeared and were shaped by interspecies transfer, it is intriguing that they could be fodder for genome building, where they provide a convenient unit of DNA that could be utilized to introduce a novel function into a synthetic organism. To date, such transfers are sometimes successful and sometimes fail for unknown reasons [7,8]. Potential problems include that the cluster may rely on regulatory interactions that are not present in the new host, the genes do not express or express at the wrong ratios, or there are auxiliary interactions with or dependencies on the host [1]. Within gene clusters, there can also be sub-gene clusters that evolve separately. This modular organization of clusters within clusters enables rapid diversification and can replicate a useful function in multiple contexts. Two examples of such sub-clusters are microcompartments that can sequester toxic metabolic intermediates (Section I.B) and the stressosome that can integrate signals and Phensuximide control different signaling mechanisms (Section V.A). Subclusters also occur within metabolic pathways, where particular conversion (e.g., the modification of a sugar moiety) can occur in different contexts. Examples of such sub-clusters are present in the erythromycin Phensuximide pathway (Section III.C). The useful functions encoded by these sub-clusters have propagated into different metabolic and signaling pathways. As the number of complete sequenced genomes grows, it has become clear that many gene clusters are cryptic; in other words, there are no known conditions under which the genes are expressed [9]. Homology analysis can be useful (albeit inexact) in predicting the general classes of molecules produces. For example, there may be many novel antibiotics and other pharmaceuticals that are encoded by such clusters. Sometimes, it is possible to wake up a cluster by engineering its regulatory circuitry [10]. This could either be through the deletion of a repressor or the addition of an inducible system. However, many clusters remain intransigent to these approaches. As the sequence databases grow, it is going to be increasingly tempting to be able to access the functions encoded therein. Genetic engineering is moving towards the era of the genome. Automated DNA synthesis has continued to advance, Phensuximide where the size of routine orders has increased to >50,000 bp, with declining cost and turnaround time [11]. Recently, the entire wild-type genome ofMycoplasmawas synthesized and transferred into a new cell, producing a living organism [12]. However, no design was implemented in this tour-de-force project; essentially, a natural genome was replicated. In an attempt to improve our design capacity, synthetic biology has been contributing a growing toolbox of genetic parts (e.g., ribosome binding sites, promoters, terminators) and devices (e.g., genetic circuits, sensors) that enable programmable control over transcription and translation [13]. In addition, methods have been developed to rapidly assemble these parts into intermediate 10kb fragments [14], which can then.