1
|
Mofayezi A, Jadaliha M, Zangeneh FZ, Khoddami V. Poly(A) tale: From A to A; RNA polyadenylation in prokaryotes and eukaryotes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1837. [PMID: 38485452 DOI: 10.1002/wrna.1837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024]
Abstract
Most eukaryotic mRNAs and different non-coding RNAs undergo a form of 3' end processing known as polyadenylation. Polyadenylation machinery is present in almost all organisms except few species. In bacteria, the machinery has evolved from PNPase, which adds heteropolymeric tails, to a poly(A)-specific polymerase. Differently, a complex machinery for accurate polyadenylation and several non-canonical poly(A) polymerases are developed in eukaryotes. The role of poly(A) tail has also evolved from serving as a degradative signal to a stabilizing modification that also regulates translation. In this review, we discuss poly(A) tail emergence in prokaryotes and its development into a stable, yet dynamic feature at the 3' end of mRNAs in eukaryotes. We also describe how appearance of novel poly(A) polymerases gives cells flexibility to shape poly(A) tail. We explain how poly(A) tail dynamics help regulate cognate RNA metabolism in a context-dependent manner, such as during oocyte maturation. Finally, we describe specific mRNAs in metazoans that bear stem-loops instead of poly(A) tails. We conclude with how recent discoveries about poly(A) tail can be applied to mRNA technology. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability.
Collapse
Affiliation(s)
- Ahmadreza Mofayezi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
- ReNAP Therapeutics, Tehran, Iran
| | - Mahdieh Jadaliha
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | | | - Vahid Khoddami
- ReNAP Therapeutics, Tehran, Iran
- Pediatric Cell and Gene Therapy Research Center, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
2
|
Liao Y. Emerging tools for uncovering genetic and transcriptomic heterogeneities in bacteria. Biophys Rev 2024; 16:109-124. [PMID: 38495445 PMCID: PMC10937887 DOI: 10.1007/s12551-023-01178-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 12/11/2023] [Indexed: 03/19/2024] Open
Abstract
Bacterial communities display an astonishing degree of heterogeneities among their constituent cells across both the genomic and transcriptomic levels, giving rise to diverse social interactions and stress-adaptation strategies indispensable for proliferating in the natural environment (Ackermann in Nat Rev Microbiol 13:497-508, 2015). Our knowledge about bacterial heterogeneities and their physiological ramifications critically depends on our ability to unambiguously resolve the genetic and phenotypic states of the individual cells that make up the population. In this short review, I highlight several recently developed methods for studying bacterial heterogeneities, primarily focusing on single-cell techniques based on advanced sequencing and microscopy technologies. I will discuss the working principle of each technique as well as the types of problems each technique is best positioned to address. With significant improvements in resolution and throughput, these emerging tools together offer unprecedented and complementary views of various types of heterogeneities found within bacterial populations, paving the way for mechanistic dissections and systematic interventions in laboratory and clinical settings.
Collapse
Affiliation(s)
- Yi Liao
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| |
Collapse
|
3
|
Xu R, Prakoso D, Salvador LCM, Rajeev S. Leptospira transcriptome sequencing using long-read technology reveals unannotated transcripts and potential polyadenylation of RNA molecules. Microbiol Spectr 2023; 11:e0223423. [PMID: 37861327 PMCID: PMC10715090 DOI: 10.1128/spectrum.02234-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023] Open
Abstract
IMPORTANCE Leptospirosis, caused by the spirochete bacteria Leptospira, is a zoonotic disease of humans and animals, accounting for over 1 million annual human cases and over 60,000 deaths. We have characterized operon transcriptional units, identified novel RNA coding regions, and reported evidence of potential posttranscriptional polyadenylation in the Leptospira transcriptomes for the first time using Oxford Nanopore Technology RNA sequencing protocols. The newly identified RNA coding regions and operon transcriptional units were detected only in the pathogenic Leptospira transcriptomes, suggesting their significance in virulence-related functions. This article integrates bioinformatics, infectious diseases, microbiology, molecular biology, veterinary sciences, and public health. Given the current knowledge gap in the regulation of leptospiral pathogenicity, our findings offer valuable insights to researchers studying leptospiral pathogenicity and provide both a basis and a tool for researchers focusing on prokaryotic molecular studies for the understanding of RNA compositions and prokaryotic polyadenylation for their organisms of interest.
Collapse
Affiliation(s)
- Ruijie Xu
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, USA
| | - Dhani Prakoso
- Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, Tennessee, USA
| | - Liliana C. M. Salvador
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Sreekumari Rajeev
- Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, Tennessee, USA
| |
Collapse
|
4
|
Yadav BNS, Sharma P, Maurya S, Yadav RK. Metagenomics and metatranscriptomics as potential driving forces for the exploration of diversity and functions of micro-eukaryotes in soil. 3 Biotech 2023; 13:423. [PMID: 38047037 PMCID: PMC10689336 DOI: 10.1007/s13205-023-03841-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
Micro-eukaryotes are ubiquitous and play vital roles in diverse ecological systems, yet their diversity and functions are scarcely known. This may be due to the limitations of formerly used conventional culture-based methods. Metagenomics and metatranscriptomics are enabling to unravel the genomic, metabolic, and phylogenetic diversity of micro-eukaryotes inhabiting in different ecosystems in a more comprehensive manner. The in-depth study of structural and functional characteristics of micro-eukaryote community residing in soil is crucial for the complete understanding of this major ecosystem. This review provides a deep insight into the methodologies employed under these approaches to study soil micro-eukaryotic organisms. Furthermore, the review describes available computational tools, pipelines, and database sources and their manipulation for the analysis of sequence data of micro-eukaryotic origin. The challenges and limitations of these approaches are also discussed in detail. In addition, this review summarizes the key findings of metagenomic and metatranscriptomic studies on soil micro-eukaryotes. It also highlights the exploitation of these methods to study the structural as well as functional profiles of soil micro-eukaryotic community and to screen functional eukaryotic protein coding genes for biotechnological applications along with the future perspectives in the field.
Collapse
Affiliation(s)
- Bhupendra Narayan Singh Yadav
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Priyanka Sharma
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Shristy Maurya
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Rajiv Kumar Yadav
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| |
Collapse
|
5
|
Contreras X, Depierre D, Akkawi C, Srbic M, Helsmoortel M, Nogaret M, LeHars M, Salifou K, Heurteau A, Cuvier O, Kiernan R. PAPγ associates with PAXT nuclear exosome to control the abundance of PROMPT ncRNAs. Nat Commun 2023; 14:6745. [PMID: 37875486 PMCID: PMC10598014 DOI: 10.1038/s41467-023-42620-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/17/2023] [Indexed: 10/26/2023] Open
Abstract
Pervasive transcription of the human genome generates an abundance of RNAs that must be processed and degraded. The nuclear RNA exosome is the main RNA degradation machinery in the nucleus. However, nuclear exosome must be recruited to its substrates by targeting complexes, such as NEXT or PAXT. By proteomic analysis, we identify additional subunits of PAXT, including many orthologs of MTREC found in S. pombe. In particular, we show that polyA polymerase gamma (PAPγ) associates with PAXT. Genome-wide mapping of the binding sites of ZFC3H1, RBM27 and PAPγ shows that PAXT is recruited to the TSS of hundreds of genes. Loss of ZFC3H1 abolishes recruitment of PAXT subunits including PAPγ to TSSs and concomitantly increases the abundance of PROMPTs at the same sites. Moreover, PAPγ, as well as MTR4 and ZFC3H1, is implicated in the polyadenylation of PROMPTs. Our results thus provide key insights into the direct targeting of PROMPT ncRNAs by PAXT at their genomic sites.
Collapse
Affiliation(s)
- Xavier Contreras
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - David Depierre
- Center of Integrative Biology (CBI-CNRS), Molecular, Cellular and Developmental Biology (MCD Unit), University of Toulouse, 31000, Toulouse, France
| | - Charbel Akkawi
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Marina Srbic
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Marion Helsmoortel
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Maguelone Nogaret
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Matthieu LeHars
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Kader Salifou
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Alexandre Heurteau
- Center of Integrative Biology (CBI-CNRS), Molecular, Cellular and Developmental Biology (MCD Unit), University of Toulouse, 31000, Toulouse, France
| | - Olivier Cuvier
- Center of Integrative Biology (CBI-CNRS), Molecular, Cellular and Developmental Biology (MCD Unit), University of Toulouse, 31000, Toulouse, France
| | - Rosemary Kiernan
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France.
| |
Collapse
|
6
|
Francis N, Behera MR, Natarajan K, Laishram RS. Tyrosine phosphorylation controlled poly(A) polymerase I activity regulates general stress response in bacteria. Life Sci Alliance 2023; 6:6/3/e202101148. [PMID: 36535710 PMCID: PMC9764084 DOI: 10.26508/lsa.202101148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
RNA 3'-end polyadenylation that marks transcripts for degradation is implicated in general stress response in Escherichia coli Yet, the mechanism and regulation of poly(A) polymerase I (PAPI) in stress response are obscure. We show that pcnB (that encodes PAPI)-null mutation widely stabilises stress response mRNAs and imparts cellular tolerance to multiple stresses, whereas PAPI ectopic expression renders cells stress-sensitive. We demonstrate that there is a substantial loss of PAPI activity on stress exposure that functionally phenocopies pcnB-null mutation stabilising target mRNAs. We identify PAPI tyrosine phosphorylation at the 202 residue (Y202) that is enormously enhanced on stress exposure. This phosphorylation inhibits PAPI polyadenylation activity under stress. Consequentially, PAPI phosphodeficient mutation (tyrosine 202 to phenylalanine, Y202F) fails to stimulate mRNA expression rendering cells stress-sensitive. Bacterial tyrosine kinase Wzc phosphorylates PAPI-Y202 residue, and that wzc-null mutation renders cells stress-sensitive. Accordingly, wzc-null mutation has no effect on stress sensitivity in the presence of pcnB-null or pcnB-Y202F mutation. We also establish that PAPI phosphorylation-dependent stress tolerance mechanism is distinct and operates downstream of the primary stress regulator RpoS.
Collapse
Affiliation(s)
- Nimmy Francis
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - Malaya R Behera
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India.,Regional Centre for Biotechnology, Faridabad, India
| | - Kathiresan Natarajan
- Transdisciplinary Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| |
Collapse
|
7
|
Hadjeras L, Bouvier M, Canal I, Poljak L, Morin-Ogier Q, Froment C, Burlet-Schlitz O, Hamouche L, Girbal L, Cocaign-Bousquet M, Carpousis AJ. Attachment of the RNA degradosome to the bacterial inner cytoplasmic membrane prevents wasteful degradation of rRNA in ribosome assembly intermediates. PLoS Biol 2023; 21:e3001942. [PMID: 36603027 PMCID: PMC9848016 DOI: 10.1371/journal.pbio.3001942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/18/2023] [Accepted: 12/01/2022] [Indexed: 01/06/2023] Open
Abstract
RNA processing and degradation shape the transcriptome by generating stable molecules that are necessary for translation (rRNA and tRNA) and by facilitating the turnover of mRNA, which is necessary for the posttranscriptional control of gene expression. In bacteria and the plant chloroplast, RNA degradosomes are multienzyme complexes that process and degrade RNA. In many bacterial species, the endoribonuclease RNase E is the central component of the RNA degradosome. RNase E-based RNA degradosomes are inner membrane proteins in a large family of gram-negative bacteria (β- and γ-Proteobacteria). Until now, the reason for membrane localization was not understood. Here, we show that a mutant strain of Escherichia coli, in which the RNA degradosome is localized to the interior of the cell, has high levels of 20S and 40S particles that are defective intermediates in ribosome assembly. These particles have aberrant protein composition and contain rRNA precursors that have been cleaved by RNase E. After RNase E cleavage, rRNA fragments are degraded to nucleotides by exoribonucleases. In vitro, rRNA in intact ribosomes is resistant to RNase E cleavage, whereas protein-free rRNA is readily degraded. We conclude that RNA degradosomes in the nucleoid of the mutant strain interfere with cotranscriptional ribosome assembly. We propose that membrane-attached RNA degradosomes in wild-type cells control the quality of ribosome assembly after intermediates are released from the nucleoid. That is, the compact structure of mature ribosomes protects rRNA against cleavage by RNase E. Turnover of a proportion of intermediates in ribosome assembly explains slow growth of the mutant strain. Competition between mRNA and rRNA degradation could be the cause of slower mRNA degradation in the mutant strain. We conclude that attachment of the RNA degradosome to the bacterial inner cytoplasmic membrane prevents wasteful degradation of rRNA precursors, thus explaining the reason for conservation of membrane-attached RNA degradosomes throughout the β- and γ-Proteobacteria.
Collapse
Affiliation(s)
- Lydia Hadjeras
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France
| | - Marie Bouvier
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France
| | - Isabelle Canal
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France
| | - Leonora Poljak
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France
| | | | - Carine Froment
- IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Infrastructure Nationale de Protéomique, ProFI, Toulouse, France
| | - Odile Burlet-Schlitz
- IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Infrastructure Nationale de Protéomique, ProFI, Toulouse, France
| | - Lina Hamouche
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France
| | - Laurence Girbal
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - Agamemnon J. Carpousis
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- * E-mail:
| |
Collapse
|
8
|
Lin D, Sutherland D, Aninta SI, Louie N, Nip KM, Li C, Yanai A, Coombe L, Warren RL, Helbing CC, Hoang LMN, Birol I. Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage. Antibiotics (Basel) 2022; 11:antibiotics11070952. [PMID: 35884206 PMCID: PMC9312091 DOI: 10.3390/antibiotics11070952] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 02/01/2023] Open
Abstract
Antibiotic resistance is a global health crisis increasing in prevalence every day. To combat this crisis, alternative antimicrobial therapeutics are urgently needed. Antimicrobial peptides (AMPs), a family of short defense proteins, are produced naturally by all organisms and hold great potential as effective alternatives to small molecule antibiotics. Here, we present rAMPage, a scalable bioinformatics discovery platform for identifying AMP sequences from RNA sequencing (RNA-seq) datasets. In our study, we demonstrate the utility and scalability of rAMPage, running it on 84 publicly available RNA-seq datasets from 75 amphibian and insect species—species known to have rich AMP repertoires. Across these datasets, we identified 1137 putative AMPs, 1024 of which were deemed novel by a homology search in cataloged AMPs in public databases. We selected 21 peptide sequences from this set for antimicrobial susceptibility testing against Escherichia coli and Staphylococcus aureus and observed that seven of them have high antimicrobial activity. Our study illustrates how in silico methods such as rAMPage can enable the fast and efficient discovery of novel antimicrobial peptides as an effective first step in the strenuous process of antimicrobial drug development.
Collapse
Affiliation(s)
- Diana Lin
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
| | - Darcy Sutherland
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, Canada;
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sambina Islam Aninta
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
| | - Nathan Louie
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
| | - Ka Ming Nip
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Chenkai Li
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Anat Yanai
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
| | - Lauren Coombe
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
| | - René L. Warren
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
| | - Caren C. Helbing
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada;
| | - Linda M. N. Hoang
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, Canada;
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Inanc Birol
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, Canada;
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Correspondence:
| |
Collapse
|
9
|
Steffen K, Laborde Q, Gunasekera S, Payne CD, Rosengren KJ, Riesgo A, Göransson U, Cárdenas P. Barrettides: A Peptide Family Specifically Produced by the Deep-Sea Sponge Geodia barretti. JOURNAL OF NATURAL PRODUCTS 2021; 84:3138-3146. [PMID: 34874154 PMCID: PMC8713285 DOI: 10.1021/acs.jnatprod.1c00938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Indexed: 05/16/2023]
Abstract
Natural product discovery by isolation and structure elucidation is a laborious task often requiring ample quantities of biological starting material and frequently resulting in the rediscovery of previously known compounds. However, peptides are a compound class amenable to an alternative genomic, transcriptomic, and in silico discovery route by similarity searches of known peptide sequences against sequencing data. Based on the sequences of barrettides A and B, we identified five new barrettide sequences (barrettides C-G) predicted from the North Atlantic deep-sea demosponge Geodia barretti (Geodiidae). We synthesized, folded, and investigated one of the newly described barrettides, barrettide C (NVVPCFCVEDETSGAKTCIPDNCDASRGTNP, disulfide connectivity I-IV, II-III). Co-elution experiments of synthetic and sponge-derived barrettide C confirmed its native conformation. NMR spectroscopy and the anti-biofouling activity on larval settlement of the bay barnacle Amphibalanus improvisus (IC50 0.64 μM) show that barrettide C is highly similar to barrettides A and B in both structure and function. Several lines of evidence suggest that barrettides are produced by the sponge itself and not one of its microbial symbionts.
Collapse
Affiliation(s)
- Karin Steffen
- Pharmacognosy,
Department of Pharmaceutical Biosciences, Biomedical Centre, Uppsala University, Husargatan 3, 751
23 Uppsala, Sweden
| | - Quentin Laborde
- Pharmacognosy,
Department of Pharmaceutical Biosciences, Biomedical Centre, Uppsala University, Husargatan 3, 751
23 Uppsala, Sweden
| | - Sunithi Gunasekera
- Pharmacognosy,
Department of Pharmaceutical Biosciences, Biomedical Centre, Uppsala University, Husargatan 3, 751
23 Uppsala, Sweden
| | - Colton D. Payne
- School
of Biomedical Sciences, The University of
Queensland, Brisbane, QLD 4072, Australia
| | - K. Johan Rosengren
- School
of Biomedical Sciences, The University of
Queensland, Brisbane, QLD 4072, Australia
| | - Ana Riesgo
- Department
of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United
Kingdom
- Department
of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales−CSIC, Calle José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Ulf Göransson
- Pharmacognosy,
Department of Pharmaceutical Biosciences, Biomedical Centre, Uppsala University, Husargatan 3, 751
23 Uppsala, Sweden
| | - Paco Cárdenas
- Pharmacognosy,
Department of Pharmaceutical Biosciences, Biomedical Centre, Uppsala University, Husargatan 3, 751
23 Uppsala, Sweden
| |
Collapse
|
10
|
Francis N, Laishram RS. Transgenesis of mammalian PABP reveals mRNA polyadenylation as a general stress response mechanism in bacteria. iScience 2021; 24:103119. [PMID: 34646982 PMCID: PMC8496165 DOI: 10.1016/j.isci.2021.103119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/23/2021] [Accepted: 09/09/2021] [Indexed: 12/01/2022] Open
Abstract
In eukaryotes, mRNA 3′-polyadenylation triggers poly(A) binding protein (PABP) recruitment and stabilization. In a stark contrast, polyadenylation marks mRNAs for degradation in bacteria. To study this difference, we trans-express the mammalian nuclear PABPN1 chromosomally and extra-chromosomally in Escherichia coli. Expression of PABPN1 but not the mutant PABPN1 stabilizes polyadenylated mRNAs and improves their half-lives. In the presence of PABPN1, 3′-exonuclease PNPase is not detected on PA-tailed mRNAs compromising the degradation. We show that PABPN1 trans-expression phenocopies pcnB (that encodes poly(A) polymerase, PAPI) mutation and regulates plasmid copy number. Genome-wide RNA-seq analysis shows a general up-regulation of polyadenylated mRNAs on PABPN1 expression, the largest subset of which are those involved in general stress response. However, major global stress regulators are unaffected on PABPN1 expression. Concomitantly, PABPN1 expression or pcnB mutation imparts cellular tolerance to multiple stresses. This study establishes mRNA 3′-polyadenylation as a general stress response mechanism in E. coli. Trans expression of mammalian PABPN1 stabilizes polyadenyated mRNAs in E. coli PABPN1 expression phenocopies pcnB mutation and regulates plasmid copy number 3′-polyadenylation acts as a general stress response mechanism in bacteria This study indicates an evolutionary significance of PABP in mRNA metabolism
Collapse
Affiliation(s)
- Nimmy Francis
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Thycaud Post, Poojappura, Trivandrum 695014, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Thycaud Post, Poojappura, Trivandrum 695014, India
| |
Collapse
|
11
|
Enhanced Prodigiosin Production in Serratia marcescens JNB5-1 by Introduction of a Polynucleotide Fragment into the pigN 3' Untranslated Region and Disulfide Bonds into O-Methyl Transferase (PigF). Appl Environ Microbiol 2021; 87:e0054321. [PMID: 34232745 DOI: 10.1128/aem.00543-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In Serratia marcescens JNB5-1, prodigiosin was highly produced at 30°C, but it was noticeably repressed at ≥37°C. Our initial results demonstrated that both the production and the stability of the O-methyl transferase (PigF) and oxidoreductase (PigN) involved in the prodigiosin pathway in S. marcescens JNB5-1 sharply decreased at ≥37°C. Therefore, in this study, we improved mRNA stability and protein production using de novo polynucleotide fragments (PNFs) and the introduction of disulfide bonds, respectively, and observed their effects on prodigiosin production. Our results demonstrate that adding PNFs at the 3' untranslated regions of pigF and pigN significantly improved the mRNA half-lives of these genes, leading to an increase in the transcript and expression levels. Subsequently, the introduction of disulfide bonds in pigF improved the thermal stability, pH stability, and copper ion resistance of PigF. Finally, shake flask fermentation showed that the prodigiosin titer with the engineered S. marcescens was increased by 61.38% from 5.36 to 8.65 g/liter compared to the JNB5-1 strain at 30°C and, significantly, the prodigiosin yield increased 2.05-fold from 0.38 to 0.78 g/liter at 37°C. In this study, we revealed that the introduction of PNFs and disulfide bonds greatly improved the expression and stability of pigF and pigN, hence efficiently enhancing prodigiosin production with S. marcescens at 30 and 37°C. IMPORTANCE This study highlights a promising strategy to improve mRNA/enzyme stability and to increase production using de novo PNF libraries and the introduction of disulfide bonds into the protein. PNFs could increase the half-life of target gene mRNA and effectively prevent its degradation. Moreover, PNFs could increase the relative intensity of target genes without affecting the expression of other genes; as a result, it could alleviate the cellular burden compared to other regulatory elements such as promoters. In addition, we obtained a PigF variant with improved activity and stability by the introduction of disulfide bonds into PigF. Collectively, we demonstrate here a novel approach for improving mRNA/enzyme stability using PNFs, which results in enhanced prodigiosin production in S. marcescens at 30°C.
Collapse
|
12
|
Jones GH. Acquisition of pcnB [poly(A) polymerase I] genes via horizontal transfer from the β, γ- Proteobacteria. Microb Genom 2021; 7. [PMID: 33502308 PMCID: PMC8208693 DOI: 10.1099/mgen.0.000508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Poly(A) polymerases (PAPs) and tRNA nucleotidyltransferases belong to a superfamily of nucleotidyltransferases and modify RNA 3'-ends. The product of the pcnB gene, PAP I, has been characterized in a few β-, γ- and δ-Proteobacteria. Using the PAP I signature sequence, putative PAPs were identified in bacterial species from the α- and ε-Proteobacteria and from four other bacterial phyla (Firmicutes, Actinobacteria, Bacteroidetes and Aquificae). Phylogenetic analysis, alien index and G+C content calculations strongly suggest that the PAPs in the species identified in this study arose by horizontal gene transfer from the β- and γ-Proteobacteria.
Collapse
Affiliation(s)
- George H Jones
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| |
Collapse
|
13
|
Cheng MY, Tao WB, Yuan BF, Feng YQ. Methods for isolation of messenger RNA from biological samples. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:289-298. [PMID: 33300893 DOI: 10.1039/d0ay01912g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
RNA molecules contain many chemical modifications that can regulate a variety of biological processes. Messenger RNA (mRNA) molecules are critical components in the central dogma of molecular biology. The discovery of reversible chemical modifications in eukaryotic mRNA brings forward a new research field in RNA modification-mediated regulation of gene expression. The modifications in mRNA generally exist in low abundance. The use of highly pure mRNA is critical for the confident identification of new modifications as well as for the accurate quantification of existing modifications in mRNA. In addition, isolation of highly pure mRNA is the first step in many biological research studies. Therefore, the methods for isolating highly pure mRNA are important for mRNA-based downstream studies. A variety of methods for isolating mRNA have been developed in the past few decades and new methods continuously emerge. This review focuses on the methodologies and protocols for isolating mRNA populations. In addition, we discuss the advantages and limitations of these methods. We hope this paper will provide a general view of mRNA isolation strategies and facilitate studies that involve mRNA modifications and functions.
Collapse
Affiliation(s)
- Ming-Yu Cheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.
| | | | | | | |
Collapse
|
14
|
Kladwang W, Topkar VV, Liu B, Rangan R, Hodges TL, Keane SC, Al-Hashimi H, Das R. Anomalous Reverse Transcription through Chemical Modifications in Polyadenosine Stretches. Biochemistry 2020; 59:2154-2170. [PMID: 32407625 DOI: 10.1021/acs.biochem.0c00020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Thermostable reverse transcriptases are workhorse enzymes underlying nearly all modern techniques for RNA structure mapping and for the transcriptome-wide discovery of RNA chemical modifications. Despite their wide use, these enzymes' behaviors at chemical modified nucleotides remain poorly understood. Wellington-Oguri et al. recently reported an apparent loss of chemical modification within putatively unstructured polyadenosine stretches modified by dimethyl sulfate or 2' hydroxyl acylation, as probed by reverse transcription. Here, reanalysis of these and other publicly available data, capillary electrophoresis experiments on chemically modified RNAs, and nuclear magnetic resonance spectroscopy on (A)12 and variants show that this effect is unlikely to arise from an unusual structure of polyadenosine. Instead, tests of different reverse transcriptases on chemically modified RNAs and molecules synthesized with single 1-methyladenosines implicate a previously uncharacterized reverse transcriptase behavior: near-quantitative bypass through chemical modifications within polyadenosine stretches. All tested natural and engineered reverse transcriptases (MMLV; SuperScript II, III, and IV; TGIRT-III; and MarathonRT) exhibit this anomalous bypass behavior. Accurate DMS-guided structure modeling of the polyadenylated HIV-1 3' untranslated region requires taking into account this anomaly. Our results suggest that poly(rA-dT) hybrid duplexes can trigger an unexpectedly effective reverse transcriptase bypass and that chemical modifications in mRNA poly(A) tails may be generally undercounted.
Collapse
Affiliation(s)
- Wipapat Kladwang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Ved V Topkar
- Biophysics Program, Stanford University, Stanford, California 94305, United States
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Ramya Rangan
- Biophysics Program, Stanford University, Stanford, California 94305, United States
| | - Tracy L Hodges
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sarah C Keane
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hashim Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States.,Department of Chemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States.,Biophysics Program, Stanford University, Stanford, California 94305, United States.,Department of Physics, Stanford University, Stanford, California 94305, United States
| |
Collapse
|
15
|
Hu JL, Liang H, Zhang H, Yang MZ, Sun W, Zhang P, Luo L, Feng JX, Bai H, Liu F, Zhang T, Yang JY, Gao Q, Long Y, Ma XY, Chen Y, Zhong Q, Yu B, Liao S, Wang Y, Zhao Y, Zeng MS, Cao N, Wang J, Chen W, Yang HT, Gao S. FAM46B is a prokaryotic-like cytoplasmic poly(A) polymerase essential in human embryonic stem cells. Nucleic Acids Res 2020; 48:2733-2748. [PMID: 32009146 PMCID: PMC7049688 DOI: 10.1093/nar/gkaa049] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/13/2020] [Accepted: 01/17/2020] [Indexed: 01/11/2023] Open
Abstract
Family with sequence similarity (FAM46) proteins are newly identified metazoan-specific poly(A) polymerases (PAPs). Although predicted as Gld-2-like eukaryotic non-canonical PAPs, the detailed architecture of FAM46 proteins is still unclear. Exact biological functions for most of FAM46 proteins also remain largely unknown. Here, we report the first crystal structure of a FAM46 protein, FAM46B. FAM46B is composed of a prominently larger N-terminal catalytic domain as compared to known eukaryotic PAPs, and a C-terminal helical domain. FAM46B resembles prokaryotic PAP/CCA-adding enzymes in overall folding as well as certain inter-domain connections, which distinguishes FAM46B from other eukaryotic non-canonical PAPs. Biochemical analysis reveals that FAM46B is an active PAP, and prefers adenosine-rich substrate RNAs. FAM46B is uniquely and highly expressed in human pre-implantation embryos and pluripotent stem cells, but sharply down-regulated following differentiation. FAM46B is localized to both cell nucleus and cytosol, and is indispensable for the viability of human embryonic stem cells. Knock-out of FAM46B is lethal. Knock-down of FAM46B induces apoptosis and restricts protein synthesis. The identification of the bacterial-like FAM46B, as a pluripotent stem cell-specific PAP involved in the maintenance of translational efficiency, provides important clues for further functional studies of this PAP in the early embryonic development of high eukaryotes.
Collapse
Affiliation(s)
- Jia-Li Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.,Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - He Liang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hong Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Ming-Zhu Yang
- MOE Key Laboratory for Stem Cells and Tissue Engineering, Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Wei Sun
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, P.R. China.,Laboratory for Functional Genomics and Systems Biology, The Berlin Institute for Medical Systems Biology, 13092 Berlin, Germany
| | - Peng Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Jian-Xiong Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Huajun Bai
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Fang Liu
- MOE Key Laboratory for Stem Cells and Tissue Engineering, Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Tianpeng Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jin-Yu Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Qingsong Gao
- Laboratory for Functional Genomics and Systems Biology, The Berlin Institute for Medical Systems Biology, 13092 Berlin, Germany
| | - Yongkang Long
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Xiao-Yan Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yang Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Qian Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Bing Yu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Shuang Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yongbo Wang
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yong Zhao
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Nan Cao
- MOE Key Laboratory for Stem Cells and Tissue Engineering, Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jichang Wang
- MOE Key Laboratory for Stem Cells and Tissue Engineering, Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Huang-Tian Yang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510530, China
| |
Collapse
|
16
|
Chakravarti LJ, Buerger P, Levin RA, van Oppen MJH. Gene regulation underpinning increased thermal tolerance in a laboratory-evolved coral photosymbiont. Mol Ecol 2020; 29:1684-1703. [PMID: 32268445 DOI: 10.1111/mec.15432] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 03/07/2020] [Accepted: 03/16/2020] [Indexed: 12/12/2022]
Abstract
Small increases in ocean temperature can disrupt the obligate symbiosis between corals and dinoflagellate microalgae, resulting in coral bleaching. Little is known about the genes that drive the physiological and bleaching response of algal symbionts to elevated temperature. Moreover, many studies to-date have compared highly divergent strains, making it challenging to accredit specific genes to contrasting traits. Here, we compare transcriptional responses at ambient (27°C) and bleaching-relevant (31°C) temperatures in a monoclonal, wild-type (WT) strain of Symbiodiniaceae to those of a selected-strain (SS), derived from the same monoclonal culture and experimentally evolved to elevated temperature over 80 generations (2.5 years). Thousands of genes were differentially expressed at a log fold-change of >8 between the WT and SS over a 35 days temperature treatment period. At 31°C, WT cells exhibited a temporally unstable transcriptomic response upregulating genes involved in the universal stress response such as molecular chaperoning, protein repair, protein degradation and DNA repair. Comparatively, SS cells exhibited a temporally stable transcriptomic response and downregulated many stress response genes that were upregulated by the WT. Among the most highly upregulated genes in the SS at 31°C were algal transcription factors and a gene probably of bacterial origin that encodes a type II secretion system protein, suggesting interactions with bacteria may contribute to the increased thermal tolerance of the SS. Genes and functional pathways conferring thermal tolerance in the SS could be targeted in future genetic engineering experiments designed to develop thermally resilient algal symbionts for use in coral restoration and conservation.
Collapse
Affiliation(s)
- Leela J Chakravarti
- Australian Institute of Marine Science, Townsville MC, Qld, Australia.,AIMS@JCU, Australian Institute of Marine Science, College of Marine and Environmental Sciences, James Cook University, Townsville, Qld, Australia.,College of Marine and Environmental Sciences, James Cook University, Townsville, Qld, Australia.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia
| | - Patrick Buerger
- CSIRO, Land & Water, Canberra, ACT, Australia.,School of BioSciences, University of Melbourne, Parkville, Vic, Australia
| | | | - Madeleine J H van Oppen
- Australian Institute of Marine Science, Townsville MC, Qld, Australia.,School of BioSciences, University of Melbourne, Parkville, Vic, Australia
| |
Collapse
|
17
|
Bead-based assay for spatiotemporal gene expression control in cell-free transcription-translation systems. Biotechniques 2020; 66:29-33. [PMID: 30730208 DOI: 10.2144/btn-2018-0097] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Cell-free gene expression has applications in synthetic biology, biotechnology and biomedicine. In this technique gene expression regulation plays an important role. Transcription factors do not completely suppress expression while other methods for expression control, for example CRISPR/Cas, often require important biochemical modifications. Here we use an all Escherichia coli-based cell-free expression system and present a bead-based method to instantly start and, at a later stage, completely stop gene expression. Magnetic beads coated with DNA of the gene of interest trigger gene expression. The expression stops if we remove the bead-bound DNA as well as transcribed mRNA by hybridization to bead-bound ssDNA. Our method is a simple way to control expression duration very accurately in time and space.
Collapse
|
18
|
Wang J, Alvin Chew BL, Lai Y, Dong H, Xu L, Balamkundu S, Cai WM, Cui L, Liu CF, Fu XY, Lin Z, Shi PY, Lu TK, Luo D, Jaffrey SR, Dedon PC. Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA. Nucleic Acids Res 2019; 47:e130. [PMID: 31504804 PMCID: PMC6847653 DOI: 10.1093/nar/gkz751] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 07/16/2019] [Accepted: 08/23/2019] [Indexed: 12/13/2022] Open
Abstract
Chemical modification of transcripts with 5' caps occurs in all organisms. Here, we report a systems-level mass spectrometry-based technique, CapQuant, for quantitative analysis of an organism's cap epitranscriptome. The method was piloted with 21 canonical caps-m7GpppN, m7GpppNm, GpppN, GpppNm, and m2,2,7GpppG-and 5 'metabolite' caps-NAD, FAD, UDP-Glc, UDP-GlcNAc, and dpCoA. Applying CapQuant to RNA from purified dengue virus, Escherichia coli, yeast, mouse tissues, and human cells, we discovered new cap structures in humans and mice (FAD, UDP-Glc, UDP-GlcNAc, and m7Gpppm6A), cell- and tissue-specific variations in cap methylation, and high proportions of caps lacking 2'-O-methylation (m7Gpppm6A in mammals, m7GpppA in dengue virus). While substantial Dimroth-induced loss of m1A and m1Am arose with specific RNA processing conditions, human lymphoblast cells showed no detectable m1A or m1Am in caps. CapQuant accurately captured the preference for purine nucleotides at eukaryotic transcription start sites and the correlation between metabolite levels and metabolite caps.
Collapse
Affiliation(s)
- Jin Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, People's Republic of China
- School of Life Sciences, Inner Mongolia University, Hohhot, People's Republic of China
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
| | - Bing Liang Alvin Chew
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- NTU Institute of Health Technologies, Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore
| | - Yong Lai
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
| | - Hongping Dong
- Shanghai Blueray Biopharma, Shanghai, People's Republic of China
| | - Luang Xu
- Cancer Science Institute of Singapore, Singapore
| | - Seetharamsingh Balamkundu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Weiling Maggie Cai
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
- Department of Microbiology, National University of Singapore, Singapore
| | - Liang Cui
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
| | - Chuan Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Xin-Yuan Fu
- Cancer Science Institute of Singapore, Singapore
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO, USA
| | - Pei-Yong Shi
- Departments of Biochemistry & Molecular Biology and Pharmacology & Toxicology, and Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Timothy K Lu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
- Synthetic Biology Center, Departments of Biological Engineering and Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
- Dept. of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| |
Collapse
|
19
|
Efficient and specific oligo-based depletion of rRNA. Sci Rep 2019; 9:12281. [PMID: 31439880 PMCID: PMC6706579 DOI: 10.1038/s41598-019-48692-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/06/2019] [Indexed: 01/09/2023] Open
Abstract
In most organisms, ribosomal RNA (rRNA) contributes to >85% of total RNA. Thus, to obtain useful information from RNA-sequencing (RNA-seq) analyses at reasonable sequencing depth, typically, mature polyadenylated transcripts are enriched or rRNA molecules are depleted. Targeted depletion of rRNA is particularly useful when studying transcripts lacking a poly(A) tail, such as some non-coding RNAs (ncRNAs), most bacterial RNAs and partially degraded or immature transcripts. While several commercially available kits allow effective rRNA depletion, their efficiency relies on a high degree of sequence homology between oligonucleotide probes and the target RNA. This restricts the use of such kits to a limited number of organisms with conserved rRNA sequences. In this study we describe the use of biotinylated oligos and streptavidin-coated paramagnetic beads for the efficient and specific depletion of trypanosomal rRNA. Our approach reduces the levels of the most abundant rRNA transcripts to less than 5% with minimal off-target effects. By adjusting the sequence of the oligonucleotide probes, our approach can be used to deplete rRNAs or other abundant transcripts independent of species. Thus, our protocol provides a useful alternative for rRNA removal where enrichment of polyadenylated transcripts is not an option and commercial kits for rRNA are not available.
Collapse
|
20
|
mRNA extraction of Xanthomonas fragariae in strawberry and validation of reference genes for the RT-qPCR for study of bacterial gene expression. Mol Biol Rep 2019; 46:5723-5733. [PMID: 31368022 DOI: 10.1007/s11033-019-05006-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/26/2019] [Indexed: 01/11/2023]
Abstract
This is the first study which describes a unique procedure of isolating of high-quality, intact RNA from strawberry leaves of Xanthomonas fragariae, three most suitable reference genes, crucial for the normalization of RT-qPCR data for this pathogen and accurate expression analysis of target genes. In our study, various mathematic algorithms: NormFinder geNorm, BestKeeper, the delta CT method, RefFinder were adopted for validation of most stable reference genes from nine candidate genes (ffh, glyA, gyrA, gyrB, proC, pykA, recA, rpoB, rpoD). The analyses allowing to select three most suitable pioneer reference genes, gyrB, ffh, and pykA, that we recommend for the normalization of RT-qPCR data and for the study of the expression of target genes in Xf. Moreover, their combination as references allowed for an accurate expression analysis and computation of the fold change of the flhF and iroN2 genes in Xf. These two genes are important for the success of the colonization of plant tissue and pathogenicity and sequences of primers designed to study these genes, are presented.
Collapse
|
21
|
Felden B, Gilot D. Modulation of Bacterial sRNAs Activity by Epigenetic Modifications: Inputs from the Eukaryotic miRNAs. Genes (Basel) 2018; 10:genes10010022. [PMID: 30602712 PMCID: PMC6356536 DOI: 10.3390/genes10010022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/18/2018] [Accepted: 12/21/2018] [Indexed: 12/14/2022] Open
Abstract
Trans-encoded bacterial regulatory RNAs (sRNAs) are functional analogues of eukaryotic microRNAs (miRNAs). These RNA classes act by base-pairing complementarity with their RNA targets to modulate gene expression (transcription, half-life and/or translation). Based on base-pairing, algorithms predict binding and the impact of small RNAs on targeted-RNAs expression and fate. However, other actors are involved such as RNA binding proteins and epigenetic modifications of the targeted and small RNAs. Post-transcriptional base modifications are widespread in all living organisms where they lower undesired RNA folds through conformation adjustments and influence RNA pairing and stability, especially if remodeling their ends. In bacteria, sRNAs possess RNA modifications either internally (methylation, pseudouridinylation) or at their ends. Nicotinamide adenine dinucleotide were detected at 5′-ends, and polyadenylation can occur at 3′-ends. Eukaryotic miRNAs possess N6-methyladenosine (m6A), A editing into I, and non-templated addition of uridines at their 3′-ends. Biological functions and enzymes involved in those sRNA and micro RNA epigenetic modifications, when known, are presented and challenged.
Collapse
Affiliation(s)
- Brice Felden
- University of Rennes 1, Inserm, BRM (Bacterial Regulatory RNAs and Medicine), UMR_S 1230, F-35043 Rennes, France.
| | - David Gilot
- CNRS UMR 6290, IGDR, University of Rennes 1, F-35043 Rennes, France.
| |
Collapse
|
22
|
Hajnsdorf E, Kaberdin VR. RNA polyadenylation and its consequences in prokaryotes. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0166. [PMID: 30397102 DOI: 10.1098/rstb.2018.0166] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2018] [Indexed: 11/12/2022] Open
Abstract
Post-transcriptional addition of poly(A) tails to the 3' end of RNA is one of the fundamental events controlling the functionality and fate of RNA in all kingdoms of life. Although an enzyme with poly(A)-adding activity was discovered in Escherichia coli more than 50 years ago, its existence and role in prokaryotic RNA metabolism were neglected for many years. As a result, it was not until 1992 that E. coli poly(A) polymerase I was purified to homogeneity and its gene was finally identified. Further work revealed that, similar to its role in surveillance of aberrant nuclear RNAs of eukaryotes, the addition of poly(A) tails often destabilizes prokaryotic RNAs and their decay intermediates, thus facilitating RNA turnover. Moreover, numerous studies carried out over the last three decades have shown that polyadenylation greatly contributes to the control of prokaryotic gene expression by affecting the steady-state level of diverse protein-coding and non-coding transcripts including antisense RNAs involved in plasmid copy number control, expression of toxin-antitoxin systems and bacteriophage development. Here, we review the main findings related to the discovery of polyadenylation in prokaryotes, isolation, and characterization and regulation of bacterial poly(A)-adding activities, and discuss the impact of polyadenylation on prokaryotic mRNA metabolism and gene expression.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
Collapse
Affiliation(s)
- Eliane Hajnsdorf
- CNRS UMR8261 associated with University Paris Diderot, Institut de Biologie Physico-Chimique, 13 rue P. et M. Curie, 75005 Paris, France
| | - Vladimir R Kaberdin
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940 Leioa, Spain .,IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain.,Research Centre for Experimental Marine Biology and Biotechnology (PIE-UPV/EHU), 48620 Plentzia, Spain
| |
Collapse
|
23
|
Tudek A, Lloret-Llinares M, Jensen TH. The multitasking polyA tail: nuclear RNA maturation, degradation and export. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0169. [PMID: 30397105 DOI: 10.1098/rstb.2018.0169] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2018] [Indexed: 12/17/2022] Open
Abstract
A polyA (pA) tail is an essential modification added to the 3' ends of a wide range of RNAs at different stages of their metabolism. Here, we describe the main sources of polyadenylation and outline their underlying biochemical interactions within the nuclei of budding yeast Saccharomyces cerevisiae, human cells and, when relevant, the fission yeast Schizosaccharomyces pombe Polyadenylation mediated by the S. cerevisiae Trf4/5 enzymes, and their human homologues PAPD5/7, typically leads to the 3'-end trimming or complete decay of non-coding RNAs. By contrast, the primary function of canonical pA polymerases (PAPs) is to produce stable and nuclear export-competent mRNAs. However, this dichotomy is becoming increasingly blurred, at least in S. pombe and human cells, where polyadenylation mediated by canonical PAPs may also result in transcript decay.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
Collapse
Affiliation(s)
- Agnieszka Tudek
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark
| | - Marta Lloret-Llinares
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark
| |
Collapse
|
24
|
Abstract
Rumen microbiome profiling uses 16S rRNA (18S rRNA, internal transcribed spacer) gene sequencing, a method that usually sequences a small portion of a single gene and is often biased and varies between different laboratories. Functional information can be inferred from this data, but only for those that are closely related to known annotated species, and even then may not truly reflect the function performed within the environment being studied. Genome sequencing of isolates and metagenome-assembled genomes has now reached a stage where representation of the majority of rumen bacterial genera are covered, but this still only represents a portion of rumen microbial species. The creation of a microbial genome (bins) database with associated functional annotations will provide a consistent reference to allow mapping of RNA-Seq reads for functional gene analysis from within the rumen microbiome. The integration of multiple omic analytics is linking functional gene activity, metabolic pathways and rumen metabolites with the responsible microbiota, supporting our biological understanding of the rumen system. The application of these techniques has advanced our understanding of the major microbial populations and functional pathways that are used in relation to lower methane emissions, higher feed efficiencies and responses to different feeding regimes. Continued and more precise use of these tools will lead to a detailed and comprehensive understanding of compositional and functional capacity and design of techniques for the directed intervention and manipulation of the rumen microbiota towards a desired state.
Collapse
|
25
|
Chrzanowska-Lightowlers Z, Rorbach J, Minczuk M. Human mitochondrial ribosomes can switch structural tRNAs - but when and why? RNA Biol 2017; 14:1668-1671. [PMID: 28786741 PMCID: PMC5731804 DOI: 10.1080/15476286.2017.1356551] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
High resolution cryoEM of mammalian mitoribosomes revealed the unexpected presence of mitochondrially encoded tRNA as a structural component of mitochondrial large ribosomal subunit (mt-LSU). Our previously published data identified that only mitochondrial (mt-) tRNAPhe and mt-tRNAVal can be incorporated into mammalian mt-LSU and within an organism there is no evidence of tissue specific variation. When mt-tRNAVal is limiting, human mitoribosomes can integrate mt-tRNAPhe instead to generate a translationally competent monosome. Here we discuss the possible reasons for and consequences of the observed plasticity of the structural mt-tRNA integration. We also indicate potential direction for further research that could help our understanding of the mechanistic and evolutionary aspects of this unprecedented system.
Collapse
Affiliation(s)
- Zofia Chrzanowska-Lightowlers
- a The Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience , Newcastle University , Newcastle upon Tyne , England , UK
| | - Joanna Rorbach
- b Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Retzius väg 8, Stockholm , Sweden
| | - Michal Minczuk
- c MRC Mitochondrial Biology Unit , Wellcome Trust/MRC Building, Hills Road, Cambridge, England , UK
| |
Collapse
|
26
|
Díez-Vives C, Moitinho-Silva L, Nielsen S, Reynolds D, Thomas T. Expression of eukaryotic-like protein in the microbiome of sponges. Mol Ecol 2017; 26:1432-1451. [PMID: 28036141 DOI: 10.1111/mec.14003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/08/2016] [Accepted: 12/09/2016] [Indexed: 01/04/2023]
Abstract
Eukaryotic-like proteins (ELPs) are classes of proteins that are found in prokaryotes, but have a likely evolutionary origin in eukaryotes. ELPs have been postulated to mediate host-microbiome interactions. Recent work has discovered that prokaryotic symbionts of sponges contain abundant and diverse genes for ELPs, which could modulate interactions with their filter-feeding and phagocytic host. However, the extent to which these ELP genes are actually used and expressed by the symbionts is poorly understood. Here, we use metatranscriptomics to investigate ELP expression in the microbiomes of three different sponges (Cymbastella concentrica, Scopalina sp. and Tedania anhelens). We developed a workflow with optimized rRNA removal and in silico subtraction of host sequences to obtain a reliable symbiont metatranscriptome. This showed that between 1.3% and 2.3% of all symbiont transcripts contain genes for ELPs. Two classes of ELPs (cadherin and tetratricopeptide repeats) were abundantly expressed in the C. concentrica and Scopalina sp. microbiomes, while ankyrin repeat ELPs were predominant in the T. anhelens metatranscriptome. Comparison with transcripts that do not encode ELPs indicated a constitutive expression of ELPs across a range of bacterial and archaeal symbionts. Expressed ELPs also contained domains involved in protein secretion and/or were co-expressed with proteins involved in extracellular transport. This suggests these ELPs are likely exported, which could allow for direct interaction with the sponge. Our study shows that ELP genes in sponge symbionts represent actively expressed functions that could mediate molecular interaction between symbiosis partners.
Collapse
Affiliation(s)
- C Díez-Vives
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
| | - L Moitinho-Silva
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
| | - S Nielsen
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
| | - D Reynolds
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
| | - T Thomas
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
27
|
Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes. Sci Rep 2017; 7:41114. [PMID: 28117413 PMCID: PMC5259769 DOI: 10.1038/srep41114] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 12/15/2016] [Indexed: 11/08/2022] Open
Abstract
Global transcriptomic analysis via RNA-seq is often hampered by the high abundance of ribosomal (r)RNA in bacterial cells. To remove rRNA and enrich coding sequences, subtractive hybridization procedures have become the approach of choice prior to RNA-seq, with their efficiency varying in a manner dependent on sample type and composition. Yet, despite an increasing number of RNA-seq studies, comparative evaluation of bacterial rRNA depletion methods has remained limited. Moreover, no such study has utilized RNA derived from bacterial biofilms, which have potentially higher rRNA:mRNA ratios and higher rRNA carryover during RNA-seq analysis. Presently, we evaluated the efficiency of three subtractive hybridization-based kits in depleting rRNA from samples derived from biofilm, as well as planktonic cells of the opportunistic human pathogen Pseudomonas aeruginosa. Our results indicated different rRNA removal efficiency for the three procedures, with the Ribo-Zero kit yielding the highest degree of rRNA depletion, which translated into enhanced enrichment of non-rRNA transcripts and increased depth of RNA-seq coverage. The results indicated that, in addition to improving RNA-seq sensitivity, efficient rRNA removal enhanced detection of low abundance transcripts via qPCR. Finally, we demonstrate that the Ribo-Zero kit also exhibited the highest efficiency when P. aeruginosa/Staphylococcus aureus co-culture RNA samples were tested.
Collapse
|
28
|
DiChiara JM, Liu B, Figaro S, Condon C, Bechhofer DH. Mapping of internal monophosphate 5' ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains. Nucleic Acids Res 2016; 44:3373-89. [PMID: 26883633 PMCID: PMC4838370 DOI: 10.1093/nar/gkw073] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 01/29/2016] [Indexed: 11/14/2022] Open
Abstract
The recent findings that the narrow-specificity endoribonuclease RNase III and the 5′ exonuclease RNase J1 are not essential in the Gram-positive model organism, Bacillus subtilis, facilitated a global analysis of internal 5′ ends that are generated or acted upon by these enzymes. An RNA-Seq protocol known as PARE (Parallel Analysis of RNA Ends) was used to capture 5′ monophosphorylated RNA ends in ribonuclease wild-type and mutant strains. Comparison of PARE peaks in strains with RNase III present or absent showed that, in addition to its well-known role in ribosomal (rRNA) processing, many coding sequences and intergenic regions appeared to be direct targets of RNase III. These target sites were, in most cases, not associated with a known antisense RNA. The PARE analysis also revealed an accumulation of 3′-proximal peaks that correlated with the absence of RNase J1, confirming the importance of RNase J1 in degrading RNA fragments that contain the transcription terminator structure. A significant result from the PARE analysis was the discovery of an endonuclease cleavage just 2 nts downstream of the 16S rRNA 3′ end. This latter observation begins to answer, at least for B. subtilis, a long-standing question on the exonucleolytic versus endonucleolytic nature of 16S rRNA maturation.
Collapse
Affiliation(s)
- Jeanne M DiChiara
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Box 1603, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Bo Liu
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Box 1603, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Sabine Figaro
- CNRS UMR8261 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Ciarán Condon
- CNRS UMR8261 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - David H Bechhofer
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Box 1603, 1 Gustave L. Levy Place, New York, NY 10029, USA
| |
Collapse
|
29
|
Rienksma RA, Suarez-Diez M, Mollenkopf HJ, Dolganov GM, Dorhoi A, Schoolnik GK, Martins Dos Santos VA, Kaufmann SH, Schaap PJ, Gengenbacher M. Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing. BMC Genomics 2015; 16:34. [PMID: 25649146 PMCID: PMC4334782 DOI: 10.1186/s12864-014-1197-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 12/22/2014] [Indexed: 02/06/2023] Open
Abstract
Background The human pathogen Mycobacterium tuberculosis has the capacity to escape eradication by professional phagocytes. During infection, M. tuberculosis resists the harsh environment of phagosomes and actively manipulates macrophages and dendritic cells to ensure prolonged intracellular survival. In contrast to other intracellular pathogens, it has remained difficult to capture the transcriptome of mycobacteria during infection due to an unfavorable host-to-pathogen ratio. Results We infected the human macrophage-like cell line THP-1 with the attenuated M. tuberculosis surrogate M. bovis Bacillus Calmette–Guérin (M. bovis BCG). Mycobacterial RNA was up to 1000-fold underrepresented in total RNA preparations of infected host cells. We employed microbial enrichment combined with specific ribosomal RNA depletion to simultaneously analyze the transcriptional responses of host and pathogen during infection by dual RNA sequencing. Our results confirm that mycobacterial pathways for cholesterol degradation and iron acquisition are upregulated during infection. In addition, genes involved in the methylcitrate cycle, aspartate metabolism and recycling of mycolic acids were induced. In response to M. bovis BCG infection, host cells upregulated de novo cholesterol biosynthesis presumably to compensate for the loss of this metabolite by bacterial catabolism. Conclusions Dual RNA sequencing allows simultaneous capture of the global transcriptome of host and pathogen, during infection. However, mycobacteria remained problematic due to their relatively low number per host cell resulting in an unfavorable bacterium-to-host RNA ratio. Here, we use a strategy that combines enrichment for bacterial transcripts and dual RNA sequencing to provide the most comprehensive transcriptome of intracellular mycobacteria to date. The knowledge acquired into the pathogen and host pathways regulated during infection may contribute to a solid basis for the deployment of novel intervention strategies to tackle infection. Electronic supplementary material The online version of this article (doi:10.1186/s12864-014-1197-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Rienk A Rienksma
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Dreijenplein 10, 6703, HB, Wageningen, the Netherlands.
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Dreijenplein 10, 6703, HB, Wageningen, the Netherlands.
| | - Hans-Joachim Mollenkopf
- Core Facility Microarray/Genomics, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany.
| | - Gregory M Dolganov
- Department of Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5124, USA.
| | - Anca Dorhoi
- Department of Immunology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany.
| | - Gary K Schoolnik
- Department of Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5124, USA.
| | - Vitor Ap Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Dreijenplein 10, 6703, HB, Wageningen, the Netherlands. .,LifeGlimmer GmbH, Markelstrasse 38, 12163, Berlin, Germany.
| | - Stefan He Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany.
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Dreijenplein 10, 6703, HB, Wageningen, the Netherlands.
| | - Martin Gengenbacher
- Department of Immunology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany. .,Present address: Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore, 117545, Singapore.
| |
Collapse
|
30
|
Laishram RS. Poly(A) polymerase (PAP) diversity in gene expression--star-PAP vs canonical PAP. FEBS Lett 2014; 588:2185-97. [PMID: 24873880 PMCID: PMC6309179 DOI: 10.1016/j.febslet.2014.05.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/02/2014] [Accepted: 05/15/2014] [Indexed: 01/09/2023]
Abstract
Almost all eukaryotic mRNAs acquire a poly(A) tail at the 3'-end by a concerted RNA processing event: cleavage and polyadenylation. The canonical PAP, PAPα, was considered the only nuclear PAP involved in general polyadenylation of mRNAs. A phosphoinositide-modulated nuclear PAP, Star-PAP, was then reported to regulate a select set of mRNAs in the cell. In addition, several non-canonical PAPs have been identified with diverse cellular functions. Further, canonical PAP itself exists in multiple isoforms thus illustrating the diversity of PAPs. In this review, we compare two nuclear PAPs, Star-PAP and PAPα with a general overview of PAP diversity in the cell. Emerging evidence suggests distinct niches of target pre-mRNAs for the two PAPs and that modulation of these PAPs regulates distinct cellular functions.
Collapse
Affiliation(s)
- Rakesh S Laishram
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.
| |
Collapse
|
31
|
|
32
|
Rorbach J, Bobrowicz A, Pearce S, Minczuk M. Polyadenylation in bacteria and organelles. Methods Mol Biol 2014; 1125:211-27. [PMID: 24590792 DOI: 10.1007/978-1-62703-971-0_18] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Polyadenylation is a posttranscriptional modification present throughout all the kingdoms of life with important roles in regulation of RNA stability, translation, and quality control. Functions of polyadenylation in prokaryotic and organellar RNA metabolism are still not fully characterized, and poly(A) tails appear to play contrasting roles in different systems. Here we present a general overview of the polyadenylation process and the factors involved in its regulation, with an emphasis on the diverse functions of 3' end modification in the control of gene expression in different biological systems.
Collapse
Affiliation(s)
- Joanna Rorbach
- Mitochondrial Genetics Group, MRC Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK,
| | | | | | | |
Collapse
|
33
|
Raabe CA, Tang TH, Brosius J, Rozhdestvensky TS. Biases in small RNA deep sequencing data. Nucleic Acids Res 2013; 42:1414-26. [PMID: 24198247 PMCID: PMC3919602 DOI: 10.1093/nar/gkt1021] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
High-throughput RNA sequencing (RNA-seq) is considered a powerful tool for novel gene discovery and fine-tuned transcriptional profiling. The digital nature of RNA-seq is also believed to simplify meta-analysis and to reduce background noise associated with hybridization-based approaches. The development of multiplex sequencing enables efficient and economic parallel analysis of gene expression. In addition, RNA-seq is of particular value when low RNA expression or modest changes between samples are monitored. However, recent data uncovered severe bias in the sequencing of small non-protein coding RNA (small RNA-seq or sRNA-seq), such that the expression levels of some RNAs appeared to be artificially enhanced and others diminished or even undetectable. The use of different adapters and barcodes during ligation as well as complex RNA structures and modifications drastically influence cDNA synthesis efficacies and exemplify sources of bias in deep sequencing. In addition, variable specific RNA G/C-content is associated with unequal polymerase chain reaction amplification efficiencies. Given the central importance of RNA-seq to molecular biology and personalized medicine, we review recent findings that challenge small non-protein coding RNA-seq data and suggest approaches and precautions to overcome or minimize bias.
Collapse
Affiliation(s)
- Carsten A Raabe
- Institute of Experimental Pathology (ZMBE), University of Muenster, Von-Esmarch-Strasse 56, 48149 Muenster, Germany and Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, 13200 Penang, Malaysia
| | | | | | | |
Collapse
|
34
|
Organism-specific rRNA capture system for application in next-generation sequencing. PLoS One 2013; 8:e74286. [PMID: 24073205 PMCID: PMC3779251 DOI: 10.1371/journal.pone.0074286] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 07/30/2013] [Indexed: 11/23/2022] Open
Abstract
RNA-sequencing is a powerful tool in studying RNomics. However, the highly abundance of ribosomal RNAs (rRNA) and transfer RNA (tRNA) have predominated in the sequencing reads, thereby hindering the study of lowly expressed genes. Therefore, rRNA depletion prior to sequencing is often performed in order to preserve the subtle alteration in gene expression especially those at relatively low expression levels. One of the commercially available methods is to use DNA or RNA probes to hybridize to the target RNAs. However, there is always a concern with the non-specific binding and unintended removal of messenger RNA (mRNA) when the same set of probes is applied to different organisms. The degree of such unintended mRNA removal varies among organisms due to organism-specific genomic variation. We developed a computer-based method to design probes to deplete rRNA in an organism-specific manner. Based on the computation results, biotinylated-RNA-probes were produced by in vitro transcription and were used to perform rRNA depletion with subtractive hybridization. We demonstrated that the designed probes of 16S rRNAs and 23S rRNAs can efficiently remove rRNAs from Mycobacterium smegmatis. In comparison with a commercial subtractive hybridization-based rRNA removal kit, using organism-specific probes is better in preserving the RNA integrity and abundance. We believe the computer-based design approach can be used as a generic method in preparing RNA of any organisms for next-generation sequencing, particularly for the transcriptome analysis of microbes.
Collapse
|
35
|
Chen IH, Cheng JH, Huang YW, Lin NS, Hsu YH, Tsai CH. Characterization of the polyadenylation activity in a replicase complex from Bamboo mosaic virus-infected Nicotiana benthamiana plants. Virology 2013; 444:64-70. [PMID: 23768785 PMCID: PMC7111917 DOI: 10.1016/j.virol.2013.05.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/20/2013] [Accepted: 05/22/2013] [Indexed: 12/30/2022]
Abstract
Bamboo mosaic virus (BaMV) has a positive-sense single-stranded RNA genome with a 5' cap and a 3' poly(A) tail. To characterize polyadenylation activity in the BaMV replicase complex, we performed the in vitro polyadenylation with various BaMV templates. We conducted a polyadenylation activity assay for BaMV RNA by using a partially purified BaMV replicase complex. The results showed that approximately 200 adenylates at the 3' end of the RNA were generated on the endogenous RNA templates. Specific fractions derived from uninfected Nicotiana benthamiana plants enhanced the polyadenylation activity, implying that host factors are involved in polyadenylation. Furthermore, polyadenylation can be detected in newly synthesized plus-strand RNA in vitro when using the exogenous BaMV minus-strand minigenome. For polyadenylation on the exogenous plus-strand minigenome, the 3' end requires at least 4A to reach 22% polyadenylation activity. The results indicate that the BaMV replicase complex recognizes the 3' end of BaMV for polyadenylation.
Collapse
Affiliation(s)
- I-Hsuan Chen
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Jai-Hong Cheng
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Ying-Wen Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Na-Sheng Lin
- The Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| |
Collapse
|
36
|
Régnier P, Hajnsdorf E. The interplay of Hfq, poly(A) polymerase I and exoribonucleases at the 3' ends of RNAs resulting from Rho-independent termination: A tentative model. RNA Biol 2013; 10:602-9. [PMID: 23392248 DOI: 10.4161/rna.23664] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Discovered in eukaryotes as a modification essential for mRNA function, polyadenylation was then identified as a means used by all cells to destabilize RNA. In Escherichia coli, most accessible 3' RNA extremities are believed to be potential targets of poly(A) polymerase I. However, some RNAs might be preferentially adenylated. After a short statement of the current knowledge of poly(A) metabolism, we discuss how Hfq could affect recognition and polyadenylation of RNA terminated by Rho-independent terminators. Comparison of RNA terminus leads to the proposal that RNAs harboring 3' terminal features required for Hfq binding are not polyadenylated, whereas those lacking these structural elements can gain the oligo(A) tails that initiate exonucleolytic degradation. We also speculate that Hfq stimulates the synthesis of longer tails that could be used as Hfq-binding sites involved in non-characterized functions of Hfq-dependent sRNAs.
Collapse
Affiliation(s)
- Philippe Régnier
- University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France.
| | | |
Collapse
|
37
|
Stewart FJ. Preparation of Microbial Community cDNA for Metatranscriptomic Analysis in Marine Plankton. Methods Enzymol 2013; 531:187-218. [DOI: 10.1016/b978-0-12-407863-5.00010-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
38
|
Xie L, Zhang L, Zhong Y, Liu N, Long Y, Wang S, Zhou X, Zhou Z, Huang Y, Wang Q. Profiling the metatranscriptome of the protistan community in Coptotermes formosanus with emphasis on the lignocellulolytic system. Genomics 2012; 99:246-55. [PMID: 22326742 DOI: 10.1016/j.ygeno.2012.01.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 01/27/2012] [Indexed: 11/19/2022]
Abstract
The symbiotic protists in the hindgut of lower termites are critical for lignocellulose decomposition. Due to the unculturability of these protists, information on lignocellulases and their abundance within the gut is unavailable. The advent of high-throughput sequencing technologies enables an investigation of the gene expression profile in this community without culturing these organisms. Here, we carried out 454 pyrosequencing to profile the metatranscriptome of the protistan community in Coptotermes formosanus. In total, 223,477 reads were obtained by sequencing the enriched protistan mRNA. Phagocytosis and cytoskeletal homeostasis pathways were highly represented in the metatranscriptome. Among the metabolic pathways, starch and sucrose metabolism were dominant. A detailed analysis combining Pfam and KEGG annotation identified 118 glycosyl hydrolases belonging to 18 different glycosyl hydrolase families (GHFs). Subsequently, a novel GHF10 endo-1,4-beta-xylanase was functionally characterized to complement our understanding of the protistan hemicellulases.
Collapse
Affiliation(s)
- Lei Xie
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Damon C, Lehembre F, Oger-Desfeux C, Luis P, Ranger J, Fraissinet-Tachet L, Marmeisse R. Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils. PLoS One 2012; 7:e28967. [PMID: 22238585 PMCID: PMC3253082 DOI: 10.1371/journal.pone.0028967] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 11/18/2011] [Indexed: 01/11/2023] Open
Abstract
Eukaryotic organisms play essential roles in the biology and fertility of soils. For example the micro and mesofauna contribute to the fragmentation and homogenization of plant organic matter, while its hydrolysis is primarily performed by the fungi. To get a global picture of the activities carried out by soil eukaryotes we sequenced 2×10,000 cDNAs synthesized from polyadenylated mRNA directly extracted from soils sampled in beech (Fagus sylvatica) and spruce (Picea abies) forests. Taxonomic affiliation of both cDNAs and 18S rRNA sequences showed a dominance of sequences from fungi (up to 60%) and metazoans while protists represented less than 12% of the 18S rRNA sequences. Sixty percent of cDNA sequences from beech forest soil and 52% from spruce forest soil had no homologs in the GenBank/EMBL/DDJB protein database. A Gene Ontology term was attributed to 39% and 31.5% of the spruce and beech soil sequences respectively. Altogether 2076 sequences were putative homologs to different enzyme classes participating to 129 KEGG pathways among which several were implicated in the utilisation of soil nutrients such as nitrogen (ammonium, amino acids, oligopeptides), sugars, phosphates and sulfate. Specific annotation of plant cell wall degrading enzymes identified enzymes active on major polymers (cellulose, hemicelluloses, pectin, lignin) and glycoside hydrolases represented 0.5% (beech soil)–0.8% (spruce soil) of the cDNAs. Other sequences coding enzymes active on organic matter (extracellular proteases, lipases, a phytase, P450 monooxygenases) were identified, thus underlining the biotechnological potential of eukaryotic metatranscriptomes. The phylogenetic affiliation of 12 full-length carbohydrate active enzymes showed that most of them were distantly related to sequences from known fungi. For example, a putative GH45 endocellulase was closely associated to molluscan sequences, while a GH7 cellobiohydrolase was closest to crustacean sequences, thus suggesting a potentially significant contribution of non-fungal eukaryotes in the actual hydrolysis of soil organic matter.
Collapse
Affiliation(s)
- Coralie Damon
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1193, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Frédéric Lehembre
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1193, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Christine Oger-Desfeux
- Pôle Rhône-Alpes de Bioinformatique, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Patricia Luis
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1193, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Jacques Ranger
- Biogéochimie des Ecosystèmes Forestiers, INRA centre de Nancy, Champenoux, France
| | - Laurence Fraissinet-Tachet
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1193, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Roland Marmeisse
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1193, Université de Lyon, Université Lyon 1, Villeurbanne, France
- * E-mail:
| |
Collapse
|
40
|
Maes A, Gracia C, Hajnsdorf E, Régnier P. Search for poly(A) polymerase targets in E. coli reveals its implication in surveillance of Glu tRNA processing and degradation of stable RNAs. Mol Microbiol 2011; 83:436-51. [PMID: 22142150 DOI: 10.1111/j.1365-2958.2011.07943.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polyadenylation is a universal post-transcriptional modification involved in degradation and quality control of bacterial RNAs. In Escherichia coli, it is admitted that any accessible RNA 3' end can be tagged by a poly(A) tail for decay. However, we do not have yet an overall view of the population of polyadenylated molecules. The sampling of polyadenylated RNAs presented here demonstrates that rRNA fragments and tRNA precursors originating from the internal spacer regions of the rrn operons, in particular, rrnB are abundant poly(A) polymerase targets. Focused analysis showed that Glu tRNA precursors originating from the rrnB and rrnG transcripts exhibit long 3' trailers that are primarily removed by PNPase and to a lesser extent by RNase II and poly(A) polymerase. Moreover, 3' trimming by exoribonucleases precedes 5' end maturation by RNase P. Interestingly, characterization of RNA fragments that accumulate in a PNPase deficient strain showed that Glu tRNA precursors still harbouring the 5' leader can be degraded by a 3' to 5' quality control pathway involving poly(A) polymerase. This demonstrates that the surveillance of tRNA maturation described for a defective tRNA also applies to a wild-type tRNA.
Collapse
Affiliation(s)
- Alexandre Maes
- CNRS UPR9073, associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | | | | | | |
Collapse
|
41
|
RNase III-dependent expression of the rpsO-pnp operon of Streptomyces coelicolor. J Bacteriol 2011; 193:4371-9. [PMID: 21742867 DOI: 10.1128/jb.00452-11] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have examined the expression of the rpsO-pnp operon in an RNase III (rnc) mutant of Streptomyces coelicolor. Western blotting demonstrated that polynucleotide phosphorylase (PNPase) levels increased in the rnc mutant, JSE1880, compared with the parental strain, M145, and this observation was confirmed by polymerization assays. It was observed that rpsO-pnp mRNA levels increased in the rnc mutant by 1.6- to 4-fold compared with M145. This increase was observed in exponential, transition, and stationary phases, and the levels of the readthrough transcript, initiated upstream of rpsO in the rpsO-pnp operon; the pnp transcript, initiated in the rpsO-pnp intergenic region; and the rpsO transcript all increased. The increased levels of these transcripts in JSE1880 reflected increased chemical half-lives for each of the three. We demonstrated further that overexpression of the rpsO-pnp operon led to significantly higher levels of PNPase activity in JSE1880 compared to M145, reflecting the likelihood that PNPase expression is autoregulated in an RNase III-dependent manner in S. coelicolor. To explore further the increase in the level of the pnp transcript initiated in the intergenic region in JSE1880, we utilized that transcript as a substrate in assays employing purified S. coelicolor RNase III. These assays revealed the presence of hitherto-undiscovered sites of RNase III cleavage of the pnp transcript. The position of those sites was determined by primer extension, and they were shown to be situated in the loops of a stem-loop structure.
Collapse
|
42
|
Ho ES, Gunderson SI. Long conserved fragments upstream of Mammalian polyadenylation sites. Genome Biol Evol 2011; 3:654-66. [PMID: 21705472 PMCID: PMC3157836 DOI: 10.1093/gbe/evr053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2011] [Indexed: 12/02/2022] Open
Abstract
Polyadenylation is a cotranscriptional nuclear RNA processing event involving endonucleolytic cleavage of the nascent, emerging pre-messenger RNA (pre-mRNA) from the RNA polymerase, immediately followed by the polymerization of adenine ribonucleotides, called the poly(A) tail, to the cleaved 3' end of the polyadenylation site (PAS). This apparently simple molecular processing step has been discovered to be connected to transcription and splicing therefore increasing its potential for regulation of gene expression. Here, through a bioinformatic analysis of cis-PAS-regulatory elements in mammals that includes taking advantage of multiple evolutionary time scales, we find unexpected selection pressure much further upstream, up to 200 nt, from the PAS than previously thought. Strikingly, close to 3,000 long (30-500 nt) noncoding conserved fragments (CFs) were discovered in the PAS flanking region of three remotely related mammalian species, human, mouse, and cow. When an even more remote transitional mammal, platypus, was included, still over a thousand CFs were found in the proximity of the PAS. Even though the biological function of these CFs remains unknown, their considerable sizes makes them unlikely to serve as protein recognition sites, which are typically ≤15 nt. By harnessing genome wide DNaseI hypersensitivity data, we have discovered that the presence of CFs correlates with chromatin accessibility. Our study is important in highlighting novel experimental targets, which may provide new understanding about the regulatory aspects of polyadenylation.
Collapse
Affiliation(s)
- Eric S. Ho
- Present address: Department of Molecular Genetics, Microbiology and Immunology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey
| | | |
Collapse
|
43
|
Importin alpha-mediated nuclear import of cytoplasmic poly(A) binding protein occurs as a direct consequence of cytoplasmic mRNA depletion. Mol Cell Biol 2011; 31:3113-25. [PMID: 21646427 DOI: 10.1128/mcb.05402-11] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Recent studies have found the cytoplasmic poly(A) binding protein (PABPC) to have opposing effects on gene expression when concentrated in the cytoplasm versus in the nucleus. PABPC is predominantly cytoplasmic at steady state, where it enhances protein synthesis through simultaneous interactions with mRNA and translation factors. However, it accumulates dramatically within the nucleus in response to various pathogenic and nonpathogenic stresses, leading to an inhibition of mRNA export. The molecular events that trigger relocalization of PABPC and the mechanisms by which it translocates into the nucleus to block gene expression are not understood. Here, we reveal an RNA-based mechanism of retaining PABPC in the cytoplasm. Expression either of viral proteins that promote mRNA turnover or of a cytoplasmic deadenylase drives nuclear relocalization of PABPC in a manner dependent on the PABPC RNA recognition motifs (RRMs). Using multiple independent binding sites within its RRMs, PABPC interacts with importin α, a component of the classical import pathway. Finally, we demonstrate that the direct association of PABPC with importin α is antagonized by the presence of poly(A) RNA, supporting a model in which RNA binding masks nuclear import signals within the PABPC RRMs, thereby ensuring efficient cytoplasmic retention of this protein in normal cells. These findings further suggest that cells must carefully calibrate the ratio of PABPC to mRNA, as events that offset this balance can dramatically influence gene expression.
Collapse
|
44
|
Richmond M, Pasupula RR, Kansara SG, Autery JP, Monk BM, Sukhodolets MV. RapA, Escherichia coli RNA polymerase SWI/SNF subunit-dependent polyadenylation of RNA. Biochemistry 2011; 50:2298-312. [PMID: 21299217 DOI: 10.1021/bi101017x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, we describe RapA-dependent polyadenylation of model RNA substrates and endogenous, RNA polymerase-associated nucleic acid fragments. We demonstrate that the Escherichia coli RNA polymerase obtained through the classic purification procedure carries endogenous RNA oligonucleotides, which, in the presence of ATP, are polyriboadenylated in a RapA-dependent manner by an accessory poly(rA) polymerase. RNA polymerase isolated from poly(A) polymerase- (PAP-) and polynucleotide phosphorylase- (PNP-) deficient E. coli strain lacks accessory (rA)(n)-synthetic activity. Experiments with reconstituted RNA polymerase-PAP and RNA polymerase-PNP mixtures suggest that RapA enables the polyadenylation by PAP of RNA polymerase-associated RNA. Mutations disrupting RapA's ATP-hydrolytic function disrupt RapA-dependent polyadenylation, and the rapA(-)E. coli strain displays a measurable reduction in RNA polyadenylation. RapA-dependent polyadenylation can also be modulated by mutations in the section of RapA's SWI/SNF domain linked to interaction with single-stranded nucleic acid. We have developed enzymatic assays in which model, synthetic RNAs are polyriboadenylated in a RapA-dependent manner. Taken together, our results are consistent with RapA acting as an RNA polymerase-associated, ATP-dependent RNA translocase. Our work further links RapA to RNA remodeling and provides new mechanistic insights into the functional interaction between RNA polymerase and RapA.
Collapse
Affiliation(s)
- Michael Richmond
- Department of Chemistry and Biochemistry, Lamar University, Beaumont, Texas 77710, United States
| | | | | | | | | | | |
Collapse
|
45
|
Chen Z, Duan X. Ribosomal RNA depletion for massively parallel bacterial RNA-sequencing applications. Methods Mol Biol 2011; 733:93-103. [PMID: 21431765 DOI: 10.1007/978-1-61779-089-8_7] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
RNA-sequencing (RNA-Seq) is a digital display of a transcriptome using next-generation sequencing technologies and provides detailed, high-throughput view of the transcriptome. The first step in RNA-Seq is to isolate whole transcriptome from total RNA. Since large ribosomal RNA (rRNA) constitutes approximately 90% RNA species in total RNA, whole transcriptome analysis without any contamination from rRNA is very difficult using existing RNA isolation methods. RiboMinus(™) purification method provides a novel and efficient method to isolate RNA molecules of the transcriptome devoid of large rRNA from total RNA for transcriptome analysis. It allows for whole transcriptome isolation through selective depletion of abundant rRNA molecules from total RNA. The rRNA depleted RNA fraction is termed as RiboMinus(™) RNA fraction, which is enriched in polyadenylated RNA, nonpolyadenylated RNA, preprocessed RNA, tRNA, numerous regulatory RNA molecules, and other RNA transcripts of yet unknown function. Using RiboMinus(™) method to isolate RiboMinus RNA results in up to 99.0% removal of 16S and 23S rRNA molecules from 0.5 to 10 μg total bacterial RNA based on Bioanalyzer analysis. It enables efficient whole transcriptome sequencing analysis without major contamination from highly abundant rRNA. Residual rRNA accounts for less than 10% of entire transcriptome based on both SOLiD and Genome Analyzer RNA-Seq data.
Collapse
|
46
|
Bechhofer DH. Bacillus subtilis mRNA decay: new parts in the toolkit. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:387-94. [PMID: 21957024 DOI: 10.1002/wrna.66] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Representatives of two new ribonuclease families have recently been discovered in the gram-positive model organism, Bacillus subtilis. The RNase J family founding members, RNase J1 and RNase J2, are highly homologous but show differential activities. Although both are broad-specificity endonucleases, only the essential RNase J1 is a 5' → 3' exonuclease-a type of ribonuclease activity that was previously thought not to exist in bacteria. Current data suggest that RNase J1 is highly involved in the turnover of mRNA decay intermediates and may also be involved in the initiation of mRNA decay. A second family of ribonucleases is represented by RNase Y, an endonuclease that exerts a large effect on global mRNA half-life. The presence of these ribonucleases in B. subtilis predicts significant differences from the well-established model of mRNA decay in Escherichia coli.
Collapse
Affiliation(s)
- David H Bechhofer
- Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY, USA.
| |
Collapse
|
47
|
Skvortsov TA, Azhikina TL. A review of the transcriptome analysis of bacterial pathogens in vivo: Problems and solutions. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:596-606. [DOI: 10.1134/s106816201005002x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
48
|
Zhang XX, Liu YH, Rainey PB. CbrAB-dependent regulation of pcnB, a poly(A) polymerase gene involved in polyadenylation of RNA in Pseudomonas fluorescens. Environ Microbiol 2010; 12:1674-83. [PMID: 20482591 DOI: 10.1111/j.1462-2920.2010.02228.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
CbrB is a global sigma(54)-dependent regulator required for nutrient acquisition in Pseudomonas. Located downstream of cbrB on the Pseudomonas fluorescens SBW25 chromosome is pcnB, a putative poly(A) polymerase gene. Presence of a sigma(54) promoter in the intergenic region of cbrB and pcnB led to the hypothesis that CbrB regulates pcnB expression in a sigma(54)-dependent manner. Here we show that transcription of pcnB is CbrB dependent. However, 5'-RACE analysis of the pcnB transcript using primers located in the pcnB coding region shows that transcription starts immediately upstream of the putative ATG site at a sigma(70)-like promoter. Deletion of pcnB caused approximately 80% decrease of ployadenylated 23S rRNA; growth of the pcnB mutant was compromised in a range of laboratory media and on sugar beet seedlings. Further 5'-RACE analysis confirmed the existence of the predicted sigma(54) promoter. Genetic analysis showed that the sigma(54) promoter drives expression of crcZ, a homologue of the recently described small RNA from Pseudomonas aeruginosa, in a CbrB-dependent manner. Taken together, our data show that both pcnB and crcZ are part of the CbrB regulon. Moreover, the data draw further attention to the central regulatory role of CbrB and provides a link between mRNA degradation and cellular catabolism.
Collapse
Affiliation(s)
- Xue-Xian Zhang
- NZ Institute for Advanced Study, Massey University Auckland, Auckland 0745, New Zealand.
| | | | | |
Collapse
|
49
|
Shih CJ, Lai MC. Differentially expressed genes after hyper- and hypo-salt stress in the halophilic archaeonMethanohalophilus portucalensis. Can J Microbiol 2010; 56:295-307. [DOI: 10.1139/w10-008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Methanohalophilus portucalensis FDF1 can grow over a range of external NaCl concentrations, from 1.2 to 2.9 mol/L. Differential gene expression in response to long-term hyper-salt stress (3.1 mol/L of NaCl) and hypo-salt stress (0.9 mol/L of NaCl) were compared by differential display RT-PCR. Fourteen differentially expressed genes responding to long-term hyper- or hypo-salt stress were detected, cloned, and sequenced. Several of the differentially expressed genes were related to the unique energy-acquiring methanogenesis pathway in this organism, including the transmembrane protein MttP, cobalamin biosynthesis protein, methenyl-H4MPT cyclohydrolase and monomethylamine methyltransferase. One signal transduction histidine kinase was identified from the hyper-salt stress cultures. Moreover, 3 known stress-response gene homologues — the DNA mismatch repair protein, MutS, the universal stress protein, UspA, and a member of the protein-disaggregating multichaperone system, ClpB — were also detected. The transcriptional analysis of these long-term salt stress response and adaptation-related genes for cells immediately after salt stress indicated that the expression of the energy metabolism genes was arrested during hyper-salt shock, while the chaperone clpB gene was stimulated by both hypo- and hyper-salt shock.
Collapse
Affiliation(s)
- Chao-Jen Shih
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| |
Collapse
|
50
|
Tartar A, Wheeler MM, Zhou X, Coy MR, Boucias DG, Scharf ME. Parallel metatranscriptome analyses of host and symbiont gene expression in the gut of the termite Reticulitermes flavipes. BIOTECHNOLOGY FOR BIOFUELS 2009; 2:25. [PMID: 19832970 PMCID: PMC2768689 DOI: 10.1186/1754-6834-2-25] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2009] [Accepted: 10/15/2009] [Indexed: 05/03/2023]
Abstract
BACKGROUND Termite lignocellulose digestion is achieved through a collaboration of host plus prokaryotic and eukaryotic symbionts. In the present work, we took a combined host and symbiont metatranscriptomic approach for investigating the digestive contributions of host and symbiont in the lower termite Reticulitermes flavipes. Our approach consisted of parallel high-throughput sequencing from (i) a host gut cDNA library and (ii) a hindgut symbiont cDNA library. Subsequently, we undertook functional analyses of newly identified phenoloxidases with potential importance as pretreatment enzymes in industrial lignocellulose processing. RESULTS Over 10,000 expressed sequence tags (ESTs) were sequenced from the 2 libraries that aligned into 6,555 putative transcripts, including 171 putative lignocellulase genes. Sequence analyses provided insights in two areas. First, a non-overlapping complement of host and symbiont (prokaryotic plus protist) glycohydrolase gene families known to participate in cellulose, hemicellulose, alpha carbohydrate, and chitin degradation were identified. Of these, cellulases are contributed by host plus symbiont genomes, whereas hemicellulases are contributed exclusively by symbiont genomes. Second, a diverse complement of previously unknown genes that encode proteins with homology to lignase, antioxidant, and detoxification enzymes were identified exclusively from the host library (laccase, catalase, peroxidase, superoxide dismutase, carboxylesterase, cytochrome P450). Subsequently, functional analyses of phenoloxidase activity provided results that were strongly consistent with patterns of laccase gene expression. In particular, phenoloxidase activity and laccase gene expression are mostly restricted to symbiont-free foregut plus salivary gland tissues, and phenoloxidase activity is inducible by lignin feeding. CONCLUSION To our knowledge, this is the first time that a dual host-symbiont transcriptome sequencing effort has been conducted in a single termite species. This sequence database represents an important new genomic resource for use in further studies of collaborative host-symbiont termite digestion, as well as development of coevolved host and symbiont-derived biocatalysts for use in industrial biomass-to-bioethanol applications. Additionally, this study demonstrates that: (i) phenoloxidase activities are prominent in the R. flavipes gut and are not symbiont derived, (ii) expands the known number of host and symbiont glycosyl hydrolase families in Reticulitermes, and (iii) supports previous models of lignin degradation and host-symbiont collaboration in cellulose/hemicellulose digestion in the termite gut. All sequences in this paper are available publicly with the accession numbers FL634956-FL640828 (Termite Gut library) and FL641015-FL645753 (Symbiont library).
Collapse
Affiliation(s)
- Aurélien Tartar
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
- Division of Math, Science and Technology, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Marsha M Wheeler
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
- Current address : Department of Entomology, University of Illinois, Champaign-Urbana, IL, USA
| | - Xuguo Zhou
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
- Current address : Department of Entomology, University of Kentucky, Lexington, KY, USA
| | - Monique R Coy
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
| | - Drion G Boucias
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
| | - Michael E Scharf
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
| |
Collapse
|