The DEAD-box RNA helicase RhlB is required for efficient RNA processing at low temperature in Caulobacter

Autor(es)

de Araujo, Hugo L. ; Picinato, Beatriz A. ; Lorenzetti, Alan P. R. ; Muthunayake, Nisansala S. ; Rathnayaka-Mudiyanselage, I. W. ; dos Santos, Naara M. ; Schrader, Jared ; Koide, Tie ; Marques, Marilis V.

• Tipo de documento: Artigo Científico
• Fonte: MICROBIOLOGY SPECTRUM; v. 11, n. 6, p. 20-pg., 2023-10-18.

Resumo

The RNA helicases from the DEAD-box family participate in several biochemical processes, with special relevance in the assembly of ribosome ribonucleoparticles and in RNA turnover as part of the multi-enzymatic RNA degradosome complex. Caulobacter crescentus has three DEAD-box RNA helicases, including RhlB, the main RNA helicase associated with the RNA degradosome. In this work, we evaluated the impact of RhlB on C. crescentus gene expression both at normal and low temperatures and its role in global RNA decay. The rhlB null mutant showed a freezing-sensitive phenotype after pre-incubation at low temperature, indicating a failure in assembling a proper cryotolerance response. A global transcriptomic profile of the wild-type and rhlB mutants was carried out at 30degree celsius and 10degree celsius and showed 73 and 477 differentially expressed genes, with the most affected gene categories being translation and posttranslational modifications. The rhlB mutant is more sensitive to streptonigrin, suggesting that the downregulation of iron-regulated genes may be due to a higher intracellular iron concentration. A high throughput screening for RhlB-binding RNAs identified 220 transcripts at 30degree celsius, and global RNA decay analyses identified several mRNAs and sRNAs that displayed altered profiles of RNA decay rates. Analyses of the transcripts' 5 '-ends from the C. crescentus rhlB mutant and from Pseudomonas aeruginosa PAO1 rhlE1 and rhlE2 mutants confirm that in the absence of the DEAD-box RNA helicase associated with RNase E, there is an accumulation of RNA degradation intermediates. IMPORTANCE One of the most important control points in gene regulation is RNA stability, which determines the half-life of a transcript from its transcription until its degradation. Bacteria have evolved a sophisticated multi-enzymatic complex, the RNA degradosome, which is dedicated mostly to RNA turnover. The combined activity of RNase E and the other RNA degradosome enzymes provides an efficient pipeline for the complete degradation of RNAs. The DEAD-box RNA helicases are very often found in RNA degradosomes from phylogenetically distant bacteria, confirming their importance in unwinding structured RNA for subsequent degradation. This work showed that the absence of the RNA helicase RhlB in the free-living Alphaproteobacterium Caulobacter crescentus causes important changes in gene expression and cell physiology. These are probably due, at least in part, to inefficient RNA processing by the RNA degradosome, particularly at low-temperature conditions. (AU)

• Processo FAPESP: 21/10577-0 - Centro de Pesquisa em Biologia de Bactérias e Bacteriófagos (CEPID B3)
• Beneficiário: Shaker Chuck Farah
• Modalidade de apoio: Auxílio à Pesquisa - Centros de Pesquisa, Inovação e Difusão - CEPIDs
• Processo FAPESP: 17/03052-2 - RNAs não codificantes derivados de sequências de inserção na arqueia halófila Halobacterium salinarum NRC-1
• Beneficiário: Alan Péricles Rodrigues Lorenzetti
• Modalidade de apoio: Bolsas no Brasil - Doutorado
• Processo FAPESP: 19/08514-0 - Complexos multienzimáticos bacterianos que regulam a homeostase celular em resposta a estresses ambientais
• Beneficiário: Marilis Do Valle Marques
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 22/00308-4 - Identificação e comparação de RNAs circulares em dados de transcritoma de arqueias
• Beneficiário: Beatriz Adas Picinato
• Modalidade de apoio: Bolsas no Brasil - Doutorado Direto
• Processo FAPESP: 22/06360-8 - Caracterização de novos circuitos regulatórios de expressão gênica em Alfaproteobactérias
• Beneficiário: Marilis Do Valle Marques
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 18/17309-8 - Estudo do papel da RNA helicase RhlB da família DEAD-box na estabilidade dos RNAs e na expressão gênica em Caulobacter crescentus
• Beneficiário: Hugo Libonati de Araújo
• Modalidade de apoio: Bolsas no Brasil - Doutorado