Archaea as a Model System for Molecular Biology and Biotechnology

Abstract

Archaea represents the third domain of life, displaying a closer relationship with eukaryotes than bacteria. These microorganisms are valuable model systems for molecular biology and biotechnology. In fact, nowadays, methanogens, halophiles, thermophilic euryarchaeota, and crenarchaeota are the four groups of archaea for which genetic systems have been well established, making them suitable as model systems and allowing for the increasing study of archaeal genes' functions. Furthermore, thermophiles are used to explore several aspects of archaeal biology, such as stress responses, DNA replication and repair, transcription, translation and its regulation mechanisms, CRISPR systems, and carbon and energy metabolism. Extremophilic archaea also represent a valuable source of new biomolecules for biological and biotechnological applications, and there is growing interest in the development of engineered strains. In this review, we report on some of the most important aspects of the use of archaea as a model system for genetic evolution, the development of genetic tools, and their application for the elucidation of the basal molecular mechanisms in this domain of life. Furthermore, an overview on the discovery of new enzymes of biotechnological interest from archaea thriving in extreme environments is reported.

Keywords: CAZymes; archaea; hyperthermophiles; metagenomic; molecular biology; recoding.

Figure 1

Schematic representation of three genome editing methods developed in H. volcanii. (A) Plasmid integration and segregation (PIS); (B) Marker replacement and looping out (MRL); (C) Marker insertion and target gene deletion (MID). In all panels, L and R arms are highlighted in blue and yellow, respectively; lacS and pyrEF genes markers are in green and teal, respectively. The pyrEF selection is used to illustrate the schemes, but any other efficient markers might be used [45]. This figure was created with BioRender.com (accessed on 7 December 2022).

Figure 2

Cas9 endonuclease recruiting for target recognition using a single chimeric RNA (A) and genome editing (B). (A) When the targeted sequence (green) is immediately followed by a PAM sequence, a single chimeric guide RNA (violet) guides the active Cas9 endonuclease (light yellow) to cleave-site-specific DNA; (B) once double strand DNA breaks are performed, cells activate error-prone non homologous end-joining (NHEJ) repair pathways to fix the damage by adding random tiny insertions (red) or deletions at the cut spot; when a homologous DNA template is available, cells can repair their DNA through a process known as homologous recombination (HR), which leads to genomic knock-in (light brown) at the exact cut region. This figure was created with BioRender.com (accessed on 7 December 2022).

Figure 3

The Pyl insertion system. Pyl, synthesized by pylB, pylD, pylC, is charged on a specific tRNA (encoded by pylT) whose anticodon AUC recognizes UAG codons. See text for details. This figure was created with BioRender.com (accessed on 7 December 2022).

Figure 4

−1 frameshifting mechanisms summarized. ORF1 is underlined in yellow. This figure was created with BioRender.com (accessed on 7 December 2022).

Figure 5

Distribution of the archaeal enzymes in the BRENDA database. (A) Relative abundances in enzymatic classes. (B) Relative abundances among the archaeal genera. Others: genera with abundance < 1%.

Figure 6

Distribution of the archaeal species in the BacDive metadatabase. (A) Phylum level. (B) Class level. Others: classes with abundances < 1%.

Figure 7

Schematic flowcharts of enzyme discovery approaches.