Identification of Hfq-binding RNAs in Caulobacter crescentus

Abstract

Small RNAs are important for post-transcriptional regulation of gene expression, affecting stability and activity of their target mRNAs. The bacterial Sm-like protein Hfq is required to promote pairing between both RNAs when their sequence complementarity is limited. To provide a first global view on the post-transcriptional landscape of the α-proteobacterium Caulobacter crescentus, we have identified the Hfq-binding RNAs employing High-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP). A total of 261 RNAs, including 3 unannotated RNAs, were successfully identified and classified according to putative function. Moreover, possible interactions between the identified sRNAs with mRNA targets were postulated through computational target predictions.

BR-bodies provide selectively permeable condensates that stimulate mRNA decay and prevent release of decay intermediates

“…Two trans-encoded sRNAs who can silence target mRNAs through base pairing were found to be slightly enriched in BR-bodies ( crfA 0.67 and chvR 0.27) (Frohlich et al, 2018; Landt et al, 2010), while another was found to be slightly depleted ( gsrN -0.24) (Tien et al, 2018). Pairing of sRNAs with mRNAs typically occurs through the Lsm protein Hfq (Santiago-Frangos and Woodson, 2018; Vogel and Luisi, 2011), and we observe that 252/257 of these RNAs that associate with Hfq (Assis et al, 2019) are enriched in BR-bodies (Table S1).…”

“…While eukaryotic RNA silencing machinery is found in P-bodies and stress granules (Hubstenberger et al, 2017; Jain et al, 2016), sRNAs were found to be enriched in BR-bodies (Fig 3A) and are known to base pair with mRNAs often through the RNA chaperone Hfq (Santiago-Frangos and Woodson, 2018; Vogel and Luisi, 2011). Indeed, Hfq bound RNAs identified by HITS-CLIP (Assis et al, 2019) including both mRNAs and sRNAs are enriched in BR-bodies (Fig S6, Table S1), suggesting mRNA silencing may be influenced by BR-body localization. Cis-encoded asRNAs were also found to be enriched in BR-bodies (Fig 3) similar to stress granules where many short asRNAs associate through pairing to their complimentary mRNAs (Van Treeck et al, 2018).…”

“…RNA-seq data used in the calculation was from C. crescentus collected in M2G minimal media (Schrader et al, 2014). Hfq HITS-CLIP RNAs used were from (Assis et al, 2019).…”

“…BR-body enrichment of Hfq associated RNAs . Box plot of BR-body enrichment Hfq bound RNAs determined by HITS-CLIP (Assis et al, 2019).…”

Environmental Conditions Modulate the Transcriptomic Response of Both Caulobacter crescentus Morphotypes to Cu Stress

“…C. crescentus harbors many small regulatory RNAs (sRNAs) that can influence gene expression at the post-transcriptional level in a variety of ways, such as direct interaction with mRNAs [ 97 , 98 ]. Differential expression of sRNAs in response to Cu was observed in all conditions, except for SW cells in PYE.…”