Arginine-rich small proteins with a domain of unknown function DUF1127 play a role in phosphate and carbon metabolism of Agrobacterium tumefaciens

The genome of Agrobacterium tumefaciens C58 harbors three genes encoding small proteins (<50 aa) with a domain of unknown function DUF1127 (ATU_RS08170, ATU_RS08175, ATU_RS21905). To investigate their function we created a triple-deletion mutant lacking those genes. Total RNA was isolated from A. tumefaciens wild type and from the triple mutant (???) at optical densities (OD) of 0.5 and 1.5, and after 24 h of growth (30 °C in YEB medium at 180 rpm) and sequenced on an Illumina platform. For data analysis, 672 small regulatory RNA (sRNA) genes annotated by Wilms et al. (1), Lee et al. (2) and Möller et al. (3) were added to the genome. At OD 0.5 a total of 76 genes showed significantly altered expression in ???. The number increased to 896 and 2,575 genes at OD 1.5 and after 24 h, respectively. 15 genes were upregulated in all three growth phases in ???. At ODs 0.5 and 1.5 numerous genes associated with glycine/serine synthesis were upregulated in the mutant. Additionally, phosphorus starvation and denitrification genes were highly induced at OD 1.5, whereas almost all sugar ABC-transporter genes were downregulated. Overall, the results demonstrate a great impact of DUF1127 proteins on the transcriptome of A. tumefaciens. 1. Wilms I, Overlöper A, Nowrousian M, Sharma CM, Narberhaus F. 2012. Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens. RNA Biol 9:446–57. 2. Lee K, Huang X, Yang C, Lee D, Ho V, Nobuta K, Fan JB, Wang K. 2013. A genome-wide survey of highly expressed non-coding RNAs and biological validation of selected candidates in Agrobacterium tumefaciens. PLoS One 8:e70720. 3. Möller P, Overlöper A, Förstner KU, Wen TN, Sharma CM, Lai EM, Narberhaus F. 2014. Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens. PLoS One 9:e110427. Overall design: Illumina RNA sequencing of the transcriptomes of Agrobacterium fabrum C58 wild type and a triple deletion mutant ?L4 (?ATU_RS21905) ?atu1667 (?ATU_RS08170) ?atu8161 (?ATU_RS08175) lacking all three short DUF1127 proteins.