Constraint and opportunity in genome innovation

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Abstract

The development of rigorous molecular taxonomy pioneered by Carl Woese has freed evolution science to explore numerous cellular activities that lead to genome change in evolution. These activities include symbiogenesis, inter- and intracellular horizontal DNA transfer, incorporation of DNA from infectious agents, and natural genetic engineering, especially the activity of mobile elements. This article reviews documented examples of all these processes and proposes experiments to extend our understanding of cell-mediated genome change.

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Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system.

Li-En Jao, Susan Wente, Wenbiao Chen (2013)

A simple and robust method for targeted mutagenesis in zebrafish has long been sought. Previous methods generate monoallelic mutations in the germ line of F0 animals, usually delaying homozygosity for the mutation to the F2 generation. Generation of robust biallelic mutations in the F0 would allow for phenotypic analysis directly in injected animals. Recently the type II prokaryotic clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) system has been adapted to serve as a targeted genome mutagenesis tool. Here we report an improved CRISPR/Cas system in zebrafish with custom guide RNAs and a zebrafish codon-optimized Cas9 protein that efficiently targeted a reporter transgene Tg(-5.1mnx1:egfp) and four endogenous loci (tyr, golden, mitfa, and ddx19). Mutagenesis rates reached 75-99%, indicating that most cells contained biallelic mutations. Recessive null-like phenotypes were observed in four of the five targeting cases, supporting high rates of biallelic gene disruption. We also observed efficient germ-line transmission of the Cas9-induced mutations. Finally, five genomic loci can be targeted simultaneously, resulting in multiple loss-of-function phenotypes in the same injected fish. This CRISPR/Cas9 system represents a highly effective and scalable gene knockout method in zebrafish and has the potential for applications in other model organisms.

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Horizontal gene transfer in eukaryotic evolution.

Patrick Keeling, Jeffrey Palmer (2008)

Horizontal gene transfer (HGT; also known as lateral gene transfer) has had an important role in eukaryotic genome evolution, but its importance is often overshadowed by the greater prevalence and our more advanced understanding of gene transfer in prokaryotes. Recurrent endosymbioses and the generally poor sampling of most nuclear genes from diverse lineages have also complicated the search for transferred genes. Nevertheless, the number of well-supported cases of transfer from both prokaryotes and eukaryotes, many with significant functional implications, is now expanding rapidly. Major recent trends include the important role of HGT in adaptation to certain specialized niches and the highly variable impact of HGT in different lineages.

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Horizontal gene transfer in prokaryotes: quantification and classification.

E. V. Koonin, K. S. Makarova, L Aravind (2001)

Comparative analysis of bacterial, archaeal, and eukaryotic genomes indicates that a significant fraction of the genes in the prokaryotic genomes have been subject to horizontal transfer. In some cases, the amount and source of horizontal gene transfer can be linked to an organism's lifestyle. For example, bacterial hyperthermophiles seem to have exchanged genes with archaea to a greater extent than other bacteria, whereas transfer of certain classes of eukaryotic genes is most common in parasitic and symbiotic bacteria. Horizontal transfer events can be classified into distinct categories of acquisition of new genes, acquisition of paralogs of existing genes, and xenologous gene displacement whereby a gene is displaced by a horizontally transferred ortholog from another lineage (xenolog). Each of these types of horizontal gene transfer is common among prokaryotes, but their relative contributions differ in different lineages. The fixation and long-term persistence of horizontally transferred genes suggests that they confer a selective advantage on the recipient organism. In most cases, the nature of this advantage remains unclear, but detailed examination of several cases of acquisition of eukaryotic genes by bacteria seems to reveal the evolutionary forces involved. Examples include isoleucyl-tRNA synthetases whose acquisition from eukaryotes by several bacteria is linked to antibiotic resistance, ATP/ADP translocases acquired by intracellular parasitic bacteria, Chlamydia and Rickettsia, apparently from plants, and proteases that may be implicated in chlamydial pathogenesis.

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Author and article information

Journal

Journal ID (nlm-ta): RNA Biol

Journal ID (iso-abbrev): RNA Biol

Journal ID (publisher-id): RNA

Title: RNA Biology

Publisher: Landes Bioscience

ISSN (Print): 1547-6286

ISSN (Electronic): 1555-8584

Publication date (Print): 01 March 2014

Publication date (Electronic): 20 December 2013

Volume: 11

Issue: 3

Pages: 186-196

Affiliations

Department of Biochemistry and Molecular Biology; University of Chicago; Chicago, IL USA

Author notes

[* ]Correspondence to: James A Shapiro, Email: jsha@ 123456uchicago.edu

Article

Publisher ID: 2013RNABIOL0220 Publisher Item ID: 27506

DOI: 10.4161/rna.27506

PMC ID: 4008547

PubMed ID: 24572460

SO-VID: bc837aea-80a5-4efe-9dc5-e422ca060fd5

License:

This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.

Constraint and opportunity in genome innovation

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Abstract

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Genome Integrity

Most cited references 210

Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system.

Horizontal gene transfer in eukaryotic evolution.

Horizontal gene transfer in prokaryotes: quantification and classification.

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