Phylogenetic analysis reveals an ancient gene duplication as the origin of the MdtABC efflux pump

Kamil Górecki1, Megan M McEvoy1,2,3

  • 1Institute for Society & Genetics, University of California, Los Angeles, California, United States of America.

Plos One
|February 13, 2020
PubMed

Insights

The MdtABC efflux pump in Gram-negative bacteria evolved from a single gene duplication event early in Proteobacteria evolution. This ancient duplication event predates major bacterial class divergences, highlighting stable bacterial pump evolution.

Area of Science:

  • Microbiology
  • Evolutionary Biology
  • Molecular Biology

Background:

  • Resistance-Nodulation-Division (RND) efflux pumps are crucial for intrinsic antibiotic resistance in Gram-negative bacteria.
  • The MdtABC pump is unique within the RND family due to its two homologous inner membrane components, MdtB and MdtC.

Purpose of the Study:

  • To investigate the evolutionary origins and phylogenetic context of the MdtBC inner membrane components within the RND family.
  • To determine the duplication event's timing and its implications for RND efflux pump evolution.

Main Methods:

  • Phylogenetic analysis of MdtBC pumps.
  • Comparative analysis with other RND efflux pumps across bacterial species.

Main Results:

  • The MdtB and MdtC inner membrane components are conserved across Proteobacterial species, originating from a single gene duplication.
  • This gene duplication event is ancient, occurring before the divergence of Alpha-, Beta-, and Gamma-Proteobacteria.
  • The MdtABC and MexMN pumps share a common ancestor, suggesting MexMN also arose from a gene duplication event.

Conclusions:

  • The MdtABC pump system has ancient evolutionary origins within the RND family.
  • Gene duplication events have played a significant role in the diversification of RND efflux pumps.
  • Core bacterial efflux pump repertoires appear evolutionarily stable.

Related Concept Videos

Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
7.7K
Exon Recombination02:32

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
Exon shuffling follows “splice frame rules.” Each exon...
4.0K
ABC Transporters: Exporter01:31

ABC Transporters: Exporter

ATP-binding cassette or ABC transporter is the largest superfamily of integral membrane proteins. The transporters have transmembrane-binding domains (TMDs) and nucleotide-binding domains (NBDs). The TMDs are specific to their substrates, whereas the NBDs are similar to engines that complete ATP hydrolysis to complete the substrate transport. They can be full transporters consisting of two TMDs and NBDs, half transporters with one TMD and NBD, while some encoded with a single TMD or NBD are...
6.1K
ABC Transporters: Importer01:27

ABC Transporters: Importer

ATP-binding cassette or ABC transporters are a class of ATP-driven pumps that hydrolyze ATP to move solutes across the membrane. They can be grouped into importers and exporters. While exporters are present in all domains of life, importers exist only in bacteria and some plants.
In bacteria, based on the number of transmembrane helices and the chemical nature of their substrates, the ABC importers can be divided into three types:
3.3K
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
8.9K
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
9.7K