Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria
Open Access
- 11 October 2019
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 47 (20), 10477-10488
- https://doi.org/10.1093/nar/gkz855
Abstract
In all cells, initiation of translation is tuned by intrinsic features of the mRNA. Here, we analyze translation in Flavobacterium johnsoniae, a representative of the Bacteroidetes. Members of this phylum naturally lack Shine–Dalgarno (SD) sequences in their mRNA, and yet their ribosomes retain the conserved anti-SD sequence. Translation initiation is tuned by mRNA secondary structure and by the identities of several key nucleotides upstream of the start codon. Positive determinants include adenine at position –3, reminiscent of the Kozak sequence of Eukarya. Comparative analysis of Escherichia coli reveals use of the same Kozak-like sequence to enhance initiation, suggesting an ancient and widespread mechanism. Elimination of contacts between A-3 and the conserved β-hairpin of ribosomal protein uS7 fails to diminish the contribution of A-3 to initiation, suggesting an indirect mode of recognition. Also, we find that, in the Bacteroidetes, the trinucleotide AUG is underrepresented in the vicinity of the start codon, which presumably helps compensate for the absence of SD sequences in these organisms.Funding Information
- National Science Foundation (MCB-1614990)
- National Institutes of Health (AI21884)
This publication has 90 references indexed in Scilit:
- Efficient translation initiation dictates codon usage at gene startMolecular Systems Biology, 2013
- The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragmentsNature Protocols, 2012
- Fast gapped-read alignment with Bowtie 2Nature Methods, 2012
- Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian ProteomesCell, 2011
- Dynamic evolution of translation initiation mechanisms in prokaryotesProceedings of the National Academy of Sciences of the United States of America, 2010
- Coordinate Regulation of Glycan Degradation and Polysaccharide Capsule Biosynthesis by a Prominent Human Gut SymbiontOnline Journal of Public Health Informatics, 2009
- Human gut microbes associated with obesityNature, 2006
- An obesity-associated gut microbiome with increased capacity for energy harvestNature, 2006
- Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collectionMolecular Systems Biology, 2006
- Obesity alters gut microbial ecologyProceedings of the National Academy of Sciences of the United States of America, 2005