Absolute Measurements of mRNA Translation in Caulobacter crescentus Reveal Important Fitness Costs of Vitamin B12 Scavenging.

James R Aretakis,Jared M Schrader,Alisa Gega,Mani Arumugam

doi:10.1128/msystems.00170-19

Abstract

Caulobacter crescentus is a model for the bacterial cell cycle which culminates in asymmetric cell division, yet little is known about the absolute levels of protein synthesis of the cellular parts needed to complete the cell cycle. Here we utilize ribosome profiling to provide absolute measurements of mRNA translation in C. crescentus, providing an important resource with quantitative genome-wide measurements of protein output across individual genes. Analysis of protein synthesis rates revealed ∼4.5% of cellular protein synthesis is for genes related to vitamin B12 import (btuB) and B12-independent methionine biosynthesis (metE) when grown in common growth media lacking B12 While its facultative B12 lifestyle provides a fitness advantage in the absence of B12, we find that it provides a fitness disadvantage of the cells in the presence of B12, potentially explaining why many Caulobacter species have lost the metE gene and become obligates for B12 IMPORTANCE Caulobacter crescentus is a model system of the bacterial cell cycle culminating in asymmetric cell division, with each daughter cell inheriting a distinct set of proteins. While a genetic network of master transcription factors coordinates the cell cycle timing of transcription for nearly 20% of Caulobacter genes, we lack knowledge of how many of each protein "part" encoded in the genome are synthesized. Therefore, to determine the absolute production rates across the genome, we performed ribosome profiling, providing, for the first time, a quantitative resource with measurements of each protein "part" needed to generate daughter cells. This resource furthers the goal of a systems-level understanding of the genetic network controlling asymmetric cell division. To highlight the utility of this data set, we probe the protein synthesis cost of a B12 utilization pathway and provide new insights into Caulobacter's adaptation to its natural environments.

Highlights

Caulobacter crescentus is a model for the bacterial cell cycle which culminates in asymmetric cell division, yet little is known about the absolute levels of protein synthesis of the cellular parts needed to complete the cell cycle
Global C. crescentus studies have focused solely on the control of the timing of gene expression in the cell cycle, and little is known about the absolute levels of protein synthesis, or how the protein synthesis resources are allocated across the proteome
We show that the facultative B12-scavenging lifestyle generates a fitness tradeoff, where in the absence of B12 there is a positive fitness advantage from MetE’s B12-independent methionine production, while in B12’s presence there is a fitness disadvantage due to the wasted cost of MetE’s protein synthesis, providing an explanation for why many isolates have lost the methionine biosynthesis (metE) gene to become obligates for B12

Summary

Introduction

Caulobacter crescentus is a model for the bacterial cell cycle which culminates in asymmetric cell division, yet little is known about the absolute levels of protein synthesis of the cellular parts needed to complete the cell cycle. To determine the absolute production rates across the genome, we performed ribosome profiling, providing, for the first time, a quantitative resource with measurements of each protein “part” needed to generate daughter cells. This resource furthers the goal of a systems-level understanding of the genetic network controlling asymmetric cell division. We show that the facultative B12-scavenging lifestyle generates a fitness tradeoff, where in the absence of B12 there is a positive fitness advantage from MetE’s B12-independent methionine production, while in B12’s presence there is a fitness disadvantage due to the wasted cost of MetE’s protein synthesis, providing an explanation for why many isolates have lost the metE gene to become obligates for B12

Methods

Results

Conclusion