Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria.

Shimon Bershtein,Jeong-Mo Choi,Jingwen Zhou,Adrian W R Serohijos,Sanchari Bhattacharyya,Eugene I Shakhnovich,Wanmeng Mu,Michael Manhart,Mark Achtman

doi:10.1371/journal.pgen.1005612

Abstract

Horizontal gene transfer (HGT) plays a central role in bacterial evolution, yet the molecular and cellular constraints on functional integration of the foreign genes are poorly understood. Here we performed inter-species replacement of the chromosomal folA gene, encoding an essential metabolic enzyme dihydrofolate reductase (DHFR), with orthologs from 35 other mesophilic bacteria. The orthologous inter-species replacements caused a marked drop (in the range 10–90%) in bacterial growth rate despite the fact that most orthologous DHFRs are as stable as E.coli DHFR at 37°C and are more catalytically active than E. coli DHFR. Although phylogenetic distance between E. coli and orthologous DHFRs as well as their individual molecular properties correlate poorly with growth rates, the product of the intracellular DHFR abundance and catalytic activity (k cat/KM), correlates strongly with growth rates, indicating that the drop in DHFR abundance constitutes the major fitness barrier to HGT. Serial propagation of the orthologous strains for ~600 generations dramatically improved growth rates by largely alleviating the fitness barriers. Whole genome sequencing and global proteome quantification revealed that the evolved strains with the largest fitness improvements have accumulated mutations that inactivated the ATP-dependent Lon protease, causing an increase in the intracellular DHFR abundance. In one case DHFR abundance increased further due to mutations accumulated in folA promoter, but only after the lon inactivating mutations were fixed in the population. Thus, by apparently distinguishing between self and non-self proteins, protein homeostasis imposes an immediate and global barrier to the functional integration of foreign genes by decreasing the intracellular abundance of their products. Once this barrier is alleviated, more fine-tuned evolution occurs to adjust the function/expression of the transferred proteins to the constraints imposed by the intracellular environment of the host organism.

Highlights

Horizontal gene transfer (HGT) is a major force in bacterial evolution [1,2,3]
Laboratory evolution resulted in an increase in orthologous dihydrofolate reductase (DHFR) abundance leading to a dramatic fitness improvement
Genomic and proteomic analyses of “naive” and evolved strains suggest a new function of protein homeostasis to discriminate between “self” and “non-self” proteins, creating fitness barriers to HGT

Summary

Introduction

Horizontal gene transfer (HGT) is a major force in bacterial evolution [1,2,3]. Comparative genomic analyses show that HGT events can be broadly classified into three types: a) acquisition of a new gene not present in the taxa, b) acquisition of an orthologous gene in addition to the endogenous chromosomal copy, and c) direct chromosomal replacement of a gene by its ortholog from other species ( known as xenologous horizontal gene transfer) [1]. The evolutionary fate of an HGT event (fixation, elimination by purifying selection, or persistence as a subdominant clone) depends on the fitness benefit or cost of the newly acquired gene Previous studies on these fitness effects have arrived at apparently inconsistent conclusions. Sorek et al [7] expressed multiple proteins from 79 prokaryotic genomes in an expression vector under control of an inducible promoter and measured the ensuing fitness effects in E. coli They found that expression of many foreign proteins is detrimental to the E. coli host and attributed the fitness cost to a gene dosage-related toxicity. Lind et al found that inter-species chromosomal replacement of three native genes encoding ribosomal proteins in S. typhimurium was detrimental to fitness, apparently due to low expression of transferred proteins [8] These studies showed that many HGT events incur fitness costs, they did not provide mechanistic or molecular explanations of why this was the case. Introduction of foreign and complex subunits in E. coli showed no loss in fitness [10]

Methods

Results

Discussion

Conclusion