Stop Codon Reassignment in the Wild

Conference · Fri Mar 21 04:00:00 EDT 2014

OSTI ID:1241187

Ivanova, Natalia ^[1]; Schwientek, Patrick ^[1]; Tripp, H. James ^[1]; Rinke, Christian ^[1]; Pati, Amrita ^[1]; Huntemann, Marcel ^[1]; Visel, Axel ^[1]; Woyke, Tanja ^[1]; Kyrpides, Nikos ^[1]; Rubin, Edward ^[1]

---

1. Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.

Since the discovery of the genetic code and protein translation mechanisms (1), a limited number of variations of the standard assignment between unique base triplets (codons) and their encoded amino acids and translational stop signals have been found in bacteria and phages (2-3). Given the apparent ubiquity of the canonical genetic code, the design of genomically recoded organisms with non-canonical codes has been suggested as a means to prevent horizontal gene transfer between laboratory and environmental organisms (4). It is also predicted that genomically recoded organisms are immune to infection by viruses, under the assumption that phages and their hosts must share a common genetic code (5). This paradigm is supported by the observation of increased resistance of genomically recoded bacteria to phages with a canonical code (4). Despite these assumptions and accompanying lines of evidence, it remains unclear whether differential and non-canonical codon usage represents an absolute barrier to phage infection and genetic exchange between organisms. Our knowledge of the diversity of genetic codes and their use by viruses and their hosts is primarily derived from the analysis of cultivated organisms. Advances in single-cell sequencing and metagenome assembly technologies have enabled the reconstruction of genomes of uncultivated bacterial and archaeal lineages (6). These initial findings suggest that large scale systematic studies of uncultivated microorganisms and viruses may reveal the extent and modes of divergence from the canonical genetic code operating in nature. To explore alternative genetic codes, we carried out a systematic analysis of stop codon reassignments from the canonical TAG amber, TGA opal, and TAA ochre codons in assembled metagenomes from environmental and host-associated samples, single-cell genomes of uncultivated bacteria and archaea, and a collection of phage sequences

• Research Organization: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC)
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 1241187
• Report Number(s): LBNL--7057E
• Country of Publication: United States
• Language: English

Related Subjects

09 BIOMASS FUELS
99 GENERAL AND MISCELLANEOUS
archaeal lineages
large scale
metagenome
microrganisms