LoaP is a broadly conserved antiterminator protein that regulates antibiotic gene clusters in Bacillus amyloliquefaciens

Goodson, Jonathan R.; Klupt, Steven; Zhang, Chengxi; Straight, Paul D.; Winkler, William E.

doi:10.1038/nmicrobiol.2017.3

Cited by 51 publications

(73 citation statements)

References 52 publications

(69 reference statements)

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“…The latest additions to antiterminator RBPs include LoaP, a Nus-like protein that promotes readthrough of intrinsic terminators in antibiotic gene clusters in Firmicutes 52 . Furthermore, two studies 53,54 have highlighted how bacteria integrate RBPs with other regulatory molecules to control antitermination.…”

Section: Antiterminationmentioning

confidence: 99%

RNA-binding proteins in bacteria

2018

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RNA-binding proteins (RBPs) are central to most if not all cellular processes, dictating the fate of virtually all RNA molecules in the cell. Starting with pioneering work on ribosomal proteins, studies of bacterial RBPs have paved the way for molecular studies of RNA-protein interactions. Work over the years has identified major RBPs that act on cellular transcripts at the various stages of bacterial gene expression and that enable their integration into post-transcriptional networks that also comprise small non-coding RNAs. Bacterial RBP research has now entered a new era in which RNA sequencing-based methods permit mapping of RBP activity in a truly global manner in vivo. Moreover, the soaring interest in understudied members of host-associated microbiota and environmental communities is likely to unveil new RBPs and to greatly expand our knowledge of RNA-protein interactions in bacteria.

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Section: Antiterminationmentioning

confidence: 99%

RNA-binding proteins in bacteria

2018

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“…Reported examples belong to a group of non-essential operon-specific proteins, all specialized paralogues of NusG (NusG SP ). They include the proteins RfaH from E. coli (Belogurov et al, 2010;Burmann et al, 2012), LoaP from Bacillus amyloliquefaciens (Goodson et al, 2017), TaA from Mixococcus xantus and the UpxY family of factors of Bacteroides (Chatzidaki-Livanis et al, 2009). Importantly, they all act in trans as processive transcriptional antiterminators, indicating the novelty of the cis-acting behaviour of PipX.…”

Section: Functional Differences Between Pipx and Other Operonspecificmentioning

confidence: 99%

The nitrogen regulator PipX acts in cis to prevent operon polarity

Cantos

Labella

Espinosa

et al. 2018

Environ Microbiol Rep

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Cyanobacteria, phototrophic organisms performing oxygenic photosynthesis, must adapt their metabolic processes to important environmental challenges, like those imposed by the succession of days and nights. Not surprisingly, certain regulatory proteins are found exclusively in this phylum. One of these unique factors, PipX, provides a mechanistic link between signals of carbon/nitrogen and of energy, transduced by the signalling protein PII, and the control of gene expression by the global nitrogen regulator NtcA. Here we report a new regulatory function of PipX: enhancement in cis of pipY expression, a gene encoding a universally conserved protein involved in amino/keto acid and Pyridoxal phosphate homeostasis. In Synechococcus elongatus and many other cyanobacteria these genes are expressed as a bicistronic pipXY operon. Despite being cis-acting, polarity suppression by PipX is nevertheless reminiscent of the function of NusG paralogues typified by RfaH, which are non-essential operon-specific bacterial factors acting in trans to upregulate horizontally-acquired genes. Furthermore, PipX and members of the NusG superfamily share a TLD/KOW structural domain, suggesting regulatory interactions of PipX with the translation machinery. Our results also suggest that the cis-acting function of PipX is a sophisticated regulatory strategy for maintaining appropriate PipX-PipY stoichiometry.

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“…ActX is encoded in the conjugative transfer operons on antibiotic-resistant plasmids in E. coli and Klebsiella pneumoniae (38). Bacillus amyloliquefaciens LoaP (39) and Myxococcus xanthus TaA (40) control production of antibiotics. Eight Bacteroides fragilis UpxY proteins are encoded within and activate capsular polysaccharide biosynthesis operons (41).…”

Section: Implications For Regulation Of Virulence and Spread Of Antibmentioning

confidence: 99%

The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand

Zuber

Schweimer

NandyMazumdar

et al. 2018

Preprint

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21RfaH, a transcription regulator of the universally conserved NusG/Spt5 family, utilizes a unique 22 mode of recruitment to elongating RNA polymerase to activate virulence genes. RfaH function 23 depends critically on an ops sequence, an exemplar of a consensus pause, in the non-template 24 DNA strand of the transcription bubble. We used structural and functional analyses to elucidate 25 the role of ops in RfaH recruitment. Our results demonstrate that ops induces pausing to facilitate 26 RfaH binding and establishes direct contacts with RfaH. Strikingly, the non-template DNA forms 27 a hairpin in the RfaH:ops complex structure, flipping out a conserved T residue that is 28 specifically recognized by RfaH. Molecular modeling and genetic evidence support the notion 29 that ops hairpin is required for RfaH recruitment. We argue that both the sequence and the 30 structure of the non-template strand are read out by transcription factors, expanding the 31 repertoire of transcriptional regulators in all domains of life. 32 33 72 (Kohler et al., 2017; Saxena et al., 2018). Following TEC dissociation, RfaH has been proposed 73 to regain the autoinhibited state (Tomar et al., 2013), thus completing the cycle. 74 A model of E. coli RfaH bound to Thermus thermophilus TEC was constructed by arbitrarily 75 threading the NT DNA (absent in the X-ray structure) through the TEC (Belogurov et al., 2007). 76 While subsequent functional analysis of RfaH supports this model (Belogurov et al., 2010), the 77 path of the NT DNA and the details of ops:RfaH interactions remain unclear. The NT DNA is 78 flexible in the TEC (Kang et al., 2017) and could be trapped in a state incompatible with 79 5 productive elongation; RfaH/NusG and yeast Spt5 have been proposed to constrain the NT 80 strand to increase processivity (Crickard et al., 2016; NandyMazumdar et al., 2016). Direct 81 contacts to the NT DNA have been demonstrated recently for Bacillus subtilis NusG (Yakhnin et 82 al., 2016) and Saccharomyces cerevisiae Spt5 (Crickard et al., 2016). 83 Here we combined structural and functional analyses to dissect RfaH:ops interactions. Our data 84 argue that ops plays two roles in RfaH recruitment: it halts RNAP to aid loading of RfaH and 85 makes specific contacts with RfaH-NTD. Strikingly, we found that a small hairpin extruded from 86 the NT DNA is required for RfaH recruitment, demonstrating how NT DNA flexibility could be 87 harnessed for transcriptional regulation in this and potentially many other systems. 88 127 pausing (Figure 2D and Figure 2 -figure supplement 1), consistent with their variability in the 128 consensus pause sequence (Figure 2A). Conversely, the G12C substitution eliminated the pause 129 at U11, making measurements of RfaH antipausing activity unreliable, but did not abrogate RfaH 130 recruitment (Figures 2C,D), suggesting that pausing at U11 is dispensable for RfaH binding 131 when RNAP is transcribing slowly. 132 Observations that RfaH is recruited to RNAP transcribing the G12C template raised a possibi...

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LoaP is a broadly conserved antiterminator protein that regulates antibiotic gene clusters in Bacillus amyloliquefaciens

Cited by 51 publications

References 52 publications

RNA-binding proteins in bacteria

RNA-binding proteins in bacteria

The nitrogen regulator PipX acts in cis to prevent operon polarity

The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand

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