Bacterial genome reductions: Tools, applications, and challenges

Abstract

Bacterial cells are widely used to produce value-added products due to their versatility, ease of manipulation, and the abundance of genome engineering tools. However, the efficiency of producing these desired biomolecules is often hindered by the cells’ own metabolism, genetic instability, and the toxicity of the product. To overcome these challenges, genome reductions have been performed, making strains with the potential of serving as chassis for downstream applications. Here we review the current technologies that enable the design and construction of such reduced-genome bacteria as well as the challenges that limit their assembly and applicability. While genomic reductions have shown improvement of many cellular characteristics, a major challenge still exists in constructing these cells efficiently and rapidly. Computational tools have been created in attempts at minimizing the time needed to design these organisms, but gaps still exist in modelling these reductions in silico. Genomic reductions are a promising avenue for improving the production of value-added products, constructing chassis cells, and for uncovering cellular function but are currently limited by their time-consuming construction methods. With improvements to and the creation of novel genome editing tools and in silico models, these approaches could be combined to expedite this process and create more streamlined and efficient cell factories.

Systematic Large Fragment Deletions in the Genome of Synechococcus elongatus and the Consequent Changes in Transcriptomic Profiles

“…However, deletions over certain ranges may cause lower growth rates [28,29], weaker environmental adaptability, poorer genetic stability [29,30], and even abnormal cell morphology [29]. Hitherto, the smallest size of a reduced bacterial genome (rather than synthetic genome) was 2.68 Mb [1,31], which is comparable in size to the Synechococcus chromosome (2.75 Mb). Although 1748 nonessential genes have been identified in Synechococcus 7942 [24], it is still unclear how many of them can be deleted stepwise.…”

“…Genome reduction refers to the removal of dispensable regions from the genome, making microbial strains more suitable for serving as a chassis for downstream applications [1]. Benefits of genome reduction include creation of a cleaner genetic background, reduced consumption of energy and resources, and increased genome stability and yields of desired products, etc.…”

“…Benefits of genome reduction include creation of a cleaner genetic background, reduced consumption of energy and resources, and increased genome stability and yields of desired products, etc. [1][2][3]. In addition to applied research and potential industrial applications, genome reduction could also be employed to investigate the functions of certain genes or metabolic pathways, genome evolution, or even the origin of life [4].…”

The Genetics of Aerotolerant Growth in a Naturally Reduced Genome Alphaproteobacterium

“…Reduced genome bacteria are powerful models for dissecting biological function and streamlined platforms for industrial production. These bacteria have less of the genetic redundancy that often obscures the functions of genes and pathways, simplifying modeling of cellular processes (1,2). Bacteria with experimentally reduced genome sizes have shown improved properties for industrial applications such as increased genomic stability (3,4), faster growth rates (5), improved transformation efficiency (6), and ease of genetic manipulation (7), all of which facilitate introduction and maintenance of engineered pathways.…”

A fitnesz-maximalizáló genomredukció lehetőségei Escherichia coli baktériumban

“…A deléciós célszekvenciák többnyire evolúciós léptékben a közelmúltban szerzett, horizontális transzferrel szerzett genomi szakaszok, mint például profágok, inszerciós szekvenciák (IS-ek). Emellett gyakori célpontok a repetitív szekvenciák, virulencia faktorok és sejtfelszíni struktúrák, a sejt védekező rendszerének elemei és genetikai diverzitásképző faktorok [29][30][31] .…”