Ribosome reinitiation at leader peptides increases translation of bacterial proteins

Part 1. RNA secondary structures of 5'-untranslated regions of proteins with the PF00270 and PF00271 domains in Corynebacterium diphtheria, C. glutamicum, and Bifidobacterium animalis. Figure S1.1. RNA duplex in the region from the stop codon of the leader gene to the start codon of the structural gene encoding helicase in C. diphtheria; Figure S1.2. RNA hairpin overlapping the Shine-Dalgarno sequence in the helicase in C. glutamicum; Figure S1.3. RNA hairpin overlapping two nucleotides of the helicase start codon in B. animalis and Streptomyces griseus. Part 2. Frequency of the leader-structural gene pairs as a function of the leader gene stop codon in Spirochaetales, Acidobacteria, Deinococcus-Thermus group, and Planctomycetes. Figure S2.1. Acidobacteria; Figure S2.2. Deinococcus–Thermus group; Figure S2.3. Planctomycetes; Figure S2.4. Spirochaetales; Figure S2.5. Actinobacteria. Part 3. Sequence logo of the 30-nt 5'-leader regions of all structural genes in Actinobacteria. (PDF 365 kb

Genetic and Genomic Analyses of Bacterial Responses to Different Stress Environments

Bacteria encounter a plethora of environmental stresses and have evolved different mechanisms to recognize and respond to various harmful conditions. Understanding and elucidating common themes as well as unique aspects of the molecular mechanisms underlying stress adaptation is important and can provide valuable strategies for applications. This study focuses on stress responses in three different bacteria, namely, Acidothermus cellulolyticus, Mycobacterium smegmatis and Escherichia coli. The thermophilic and acidophilic organism A. cellulolyticus was used as a model system to understand the effects of lignin phenolic acids on cellulolytic bacteria. Lignin phenolic acids pose a significant challenge to microbial deconstruction of lignocellulosic biomass for the commercial production of renewable products. Analysis of total proteins profiles of A. cellulolyticus revealed the enhanced expression of a predicted thiosulfate sulfurtransferase (TST) protein (Acel_0059) during exposure to phenolic acids. Expression of genes involved in sulfur assimilation into cysteine was also upregulated in the presence of phenolic acids. Heterologous expression of the Acel_0059 gene in E. coli alleviated growth inhibition of inhibitory phenolic acids. Analyses of the whole transcriptome of A. cellulolyticus revealed that exposure to these inhibitory lignin components induced the expression of genes coding for membrane proteins, efflux and transport proteins, oxidative stress response proteins, redox-sensors, TST, and sulfur assimilation pathway enzymes. Deletion of the Acel_0059 counterpart gene (MSMEG_5879) in a surrogate host M. smegmatis increased the sensitivity of the organism to a variety of stressors. The deletion of TST gene affected cysteine biosynthesis from inorganic sulfate under hypoxic conditions in M. smegmatis. In another study, E. coli was used as a model to assess the biological effects of oxidized graphene (OG), a carbon nanomaterial. Growth analysis revealed that the addition of OG inhibited the growth of E. coli. Analyses of the whole transcriptome of E. coli showed that the cytotoxicity of OG in E. coli could be attributed to oxidative stress, membrane stress and DNA damage. Overall the above studies provided new insights into the shared (eg. sulfur metabolism, oxidative stress adaptation) as well as unique (eg. TST, membrane proteins) aspects of bacterial responses to diverse stresses