The Nature's Novel Ways To Genetically Modify Organisms
Author: Vipin Chandra Kalia

Introduction

Evolution of living beings happens largely through modification and/or exchange of genetic material. In general, the transfer of genetic material occurs between parents and their offspring. The process is termed as vertical gene transfer i.e. vertical inheritance. In contrast, transfer of genetic material can also take place directly between two genomes, especially among distantly related organisms. This pattern of Horizontal Gene Transfer (HGT) is called as horizontal inheritance.

The mechanisms of HGT

i. Conjugation : DNA is transferred from one organism to another through the exchange of plasmid.

ii. Transduction : In this case, bacteriophages assist in transmitting DNA.

iii. Transformation : Bacteria uptake DNA material available in its vicinity. These cells are called as competent cells as they can bind DNA to their surface and transport it through the cell envelope. DNA thus gets integrated into the recipient cell and operates through host machinery.

Detecting HGT

i. Phylogenetic discrepancy

Phylogenetic tree based on gene sequence of closely related organism have a high similarity and is indicated by high BootStrap Values (BV). BVs higher than 80-85% similarity index are indicative of vertical inheritance. Higher incongruencies in BV are potential cases of HGT. Such phylogenetic incongruencies may happen also because of events such as gene loss, gene duplication, gene conversion, recombinations or mosaics. To distinguish between apparent and real cases of HGT, we need to look for other evidences.

ii. Synteny

In general, the genes are arranged on the genetic material as operon or in the vicinity of each other depending upon their need to participate in a metabolic pathway or network. This gene order is maintained within closely related species. A comparison of the gene in question and the genes on either side can prove helpful in supporting HGT.

iii. GC content

The G+C content of a gene and that of the genome shows high congruency. However, in the case a gene has been transferred through HGT, its G+C content deviates significantly from that of the host genome.

iv. Codon Adaptation Index (CAI)

Once a gene gets integrated into the genome, it changes of the codons to match with the rest of genome. It is a measurement of the adaptation of the codon usage of a gene towards those used by highly expressed genes. The CAI values range on the scale from 0-1. A CAI value of a gene between 0.8 and 1.0 indicates higher proportion of the codons which are the most abundant.

Genetic significance of HGT

Basically, it allows a much rapid evolution. In Nature, eukaryotic chloroplast and mitochondria represent HGT, where bacteria genomes merged into eukaryotes and are the present day endosymbiotes. Protists represent a case of multiple endosymbioses. According to different estimates up to 60% of the prokaryotic genes have been influenced by HGT. Organisms withstand HGT, primarily if it confers beneficial functions to the host. It provides selective advantages to the host by enabling the functioning of novel metabolic abilities, which result in better survival. In Salmonella typhimurium, biosynthetic pathway involving cobalmin (Coenzyme B12) biosynthetic operon and degradative pathways for propanediol metabolism (pdu operon), represent a case which shows gain of functions through HGT. Tryptophan biosynthetic pathways of Brevibacterium lactofermentum and eneteric bacteria reflect loss and gain of genes. Compared to chance detection of HGT, whole genome sequences have also provided evidences of HGT – Archael and bacterial hyperthermophiles, pathogens such as Rickettsia and Chlamydia, which have genes indicative of their adaptation to the environment.

Extent of HGT

Microbes, which are parasitic in nature shed their genes and retain the moist important genes. As a consequence, they have much smaller genomes – Rickettsia prowazekii, Borrelia burgdoferi andMycoplasma genitalium, are have virtually no HGT events. Synechocystis spp. have acquired 17% of their genome through HGT. Other cases with high HGT cases are represented byEscherichia coli, Methanococcus jannaschii, Archaeoglobus fulgidus and Bacillus subtilis.


Biotechnological significance of HGT

Most efforts to genetically modify organisms fail because we select a gene or genes of our interest and virtually force the host cell to accept it. Host cells may not accept the foreign genetic material and reject it as it is not compatible with its genetic machinery. Genes, which have undergone horizontal transfer and have been accepted and adapted by the host are much likely candidates for producing GMOs. This process opens up avenues for transforming non-producers or inefficient producers of a particular product to a producer status.

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About Author / Additional Info:
Researcher in Microbial Biotechnology and Genomics at CSIR-IGIB, Delhi.