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Li Z, Liu X, Ning N, Li T, Wang H. Diversity, Distribution, and Chromosomal Rearrangements of TRIP1 Repeat Sequences in Escherichia coli. Genes (Basel) 2024; 15:236. [PMID: 38397225 PMCID: PMC10888264 DOI: 10.3390/genes15020236] [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: 01/17/2024] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
The bacterial genome contains numerous repeated sequences that greatly affect its genomic plasticity. The Escherichia coli K-12 genome contains three copies of the TRIP1 repeat sequence (TRIP1a, TRIP1b, and TRIP1c). However, the diversity, distribution, and role of the TRIP1 repeat sequence in the E. coli genome are still unclear. In this study, after screening 6725 E. coli genomes, the TRIP1 repeat was found in the majority of E. coli strains (96%: 6454/6725). The copy number and direction of the TRIP1 repeat sequence varied in each genome. Overall, 2449 genomes (36%: 2449/6725) had three copies of TRIP1 (TRIP1a, TRIP1b, and TRIP1c), which is the same as E. coli K-12. Five types of TRIP1 repeats, including two new types (TRIP1d and TRIP1e), are identified in E. coli genomes, located in 4703, 3529, 5741, 1565, and 232 genomes, respectively. Each type of TRIP1 repeat is localized to a specific locus on the chromosome. TRIP1 repeats can cause intra-chromosomal rearrangements. A total of 156 rearrangement events were identified, of which 88% (137/156) were between TRIP1a and TRIP1c. These findings have important implications for future research on TRIP1 repeats.
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Affiliation(s)
- Zhan Li
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing 100071, China; (Z.L.); (N.N.); (T.L.)
| | - Xiong Liu
- Chinese PLA Center for Disease Control and Prevention, Dongda Street 20#, Fengtai District, Beijing 100071, China;
| | - Nianzhi Ning
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing 100071, China; (Z.L.); (N.N.); (T.L.)
| | - Tao Li
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing 100071, China; (Z.L.); (N.N.); (T.L.)
| | - Hui Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing 100071, China; (Z.L.); (N.N.); (T.L.)
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2
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Teng Z, Pan X, Liu Y, You J, Zhang H, Zhao Z, Qiao Z, Rao Z. Engineering serine hydroxymethyltransferases for efficient synthesis of L-serine in Escherichia coli. BIORESOURCE TECHNOLOGY 2024; 393:130153. [PMID: 38052329 DOI: 10.1016/j.biortech.2023.130153] [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: 11/13/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 12/07/2023]
Abstract
L-serine is a high-value amino acid widely used in the food, medicine, and cosmetic industries. However, the low yield of L-serine has limited its industrial production. In this study, a cellular factory for efficient synthesis of L-serine was obtained by engineering the serine hydroxymethyltransferases (SHMT). Firstly, after screening the SHMT from Alcanivorax dieselolei by genome mining, a mutant AdSHMTE266M with high thermal stability was identified through rational design. Subsequently, an iterative saturating mutant library was constructed by using coevolutionary analysis, and a mutant AdSHMTE160L/E193Q with enzyme activity 1.35 times higher than AdSHMT was identified. Additionally, the target protein AdSHMTE160L/E193Q/E266M was efficiently overexpressed by improving its mRNA stability. Finally, combining the substrate addition strategy and system optimization, the optimized strain BL21/pET28a-AdSHMTE160L/E193Q/E266M-5'UTR-REP3S16 produced 106.06 g/L L-serine, which is the highest production to date. This study provides new ideas and insights for the engineering design of SHMT and the industrial production of L-serine.
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Affiliation(s)
- Zixin Teng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Yunran Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Jiajia You
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Hengwei Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhenqiang Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhina Qiao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China.
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3
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Bertels F, Rainey PB. Ancient Darwinian replicators nested within eubacterial genomes. Bioessays 2023; 45:e2200085. [PMID: 36456469 DOI: 10.1002/bies.202200085] [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: 04/29/2022] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022]
Abstract
Integrative mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages are short. For long-term survival, MGEs must continuously invade new hosts by horizontal transfer. Theoretically, MGEs that persist for millions of years in single lineages, and are thus subject to vertical inheritance, should not exist. Here we draw attention to an exception - a class of MGE termed REPIN. REPINs are non-autonomous MGEs whose duplication depends on non-jumping RAYT transposases. Comparisons of REPINs and typical MGEs show that replication rates of REPINs are orders of magnitude lower, REPIN population size fluctuations correlate with changes in available genome space, REPIN conservation depends on RAYT function, and REPIN diversity accumulates within host lineages. These data lead to the hypothesis that REPINs form enduring, beneficial associations with eubacterial chromosomes. Given replicative nesting, our hypothesis predicts conflicts arising from the diverging effects of selection acting simultaneously on REPINs and host genomes. Evidence in support comes from patterns of REPIN abundance and diversity in two distantly related bacterial species. Together this bolsters the conclusion that REPINs are the genetic counterpart of mutualistic endosymbiotic bacteria.
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Affiliation(s)
- Frederic Bertels
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Laboratory of Biophysics and Evolution, CBI, ESPCI Paris, Université PSL, CNRS, Paris, France
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4
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Mechanisms Affecting the Biosynthesis and Incorporation Rate of Selenocysteine. Molecules 2021; 26:molecules26237120. [PMID: 34885702 PMCID: PMC8659212 DOI: 10.3390/molecules26237120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/12/2021] [Accepted: 11/18/2021] [Indexed: 11/17/2022] Open
Abstract
Selenocysteine (Sec) is the 21st non-standard proteinogenic amino acid. Due to the particularity of the codon encoding Sec, the selenoprotein synthesis needs to be completed by unique mechanisms in specific biological systems. In this paper, the underlying mechanisms for the biosynthesis and incorporation of Sec into selenoprotein were comprehensively reviewed on five aspects: (i) the specific biosynthesis mechanism of Sec and the role of its internal influencing factors (SelA, SelB, SelC, SelD, SPS2 and PSTK); (ii) the elements (SECIS, PSL, SPUR and RF) on mRNA and their functional mechanisms; (iii) the specificity (either translation termination or translation into Sec) of UGA; (iv) the structure–activity relationship and action mechanism of SelA, SelB, SelC and SelD; and (v) the operating mechanism of two key enzyme systems for inorganic selenium source flow before Sec synthesis. Lastly, the size of the translation initiation interval, other action modes of SECIS and effects of REPS (Repetitive Extragenic Palindromic Sequences) that affect the incorporation efficiency of Sec was also discussed to provide scientific basis for the large-scale industrial fermentation for the production of selenoprotein.
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5
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Gómez-García G, Ruiz-Enamorado A, Yuste L, Rojo F, Moreno R. Expression of the ISPpu9 transposase of Pseudomonas putida KT2440 is regulated by two small RNAs and the secondary structure of the mRNA 5'-untranslated region. Nucleic Acids Res 2021; 49:9211-9228. [PMID: 34379788 PMCID: PMC8450116 DOI: 10.1093/nar/gkab672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/23/2021] [Accepted: 07/26/2021] [Indexed: 11/20/2022] Open
Abstract
Insertion sequences (ISs) are mobile genetic elements that only carry the information required for their own transposition. Pseudomonas putida KT2440, a model bacterium, has seven copies of an IS called ISPpu9 inserted into repetitive extragenic palindromic sequences. This work shows that the gene for ISPpu9 transposase, tnp, is regulated by two small RNAs (sRNAs) named Asr9 and Ssr9, which are encoded upstream and downstream of tnp, respectively. The tnp mRNA has a long 5′-untranslated region (5′-UTR) that can fold into a secondary structure that likely includes the ribosome-binding site (RBS). Mutations weakening this structure increased tnp mRNA translation. Asr9, an antisense sRNA complementary to the 5′-UTR, was shown to be very stable. Eliminating Asr9 considerably reduced tnp mRNA translation, suggesting that it helps to unfold this secondary structure, exposing the RBS. Ectopic overproduction of Asr9 increased the transposition frequency of a new ISPpu9 entering the cell by conjugation, suggesting improved tnp expression. Ssr9 has significant complementarity to Asr9 and annealed to it in vitro forming an RNA duplex; this would sequester it and possibly facilitate its degradation. Thus, the antisense Asr9 sRNA likely facilitates tnp expression, improving transposition, while Ssr9 might counteract Asr9, keeping tnp expression low.
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Affiliation(s)
- Guillermo Gómez-García
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Angel Ruiz-Enamorado
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Luis Yuste
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Fernando Rojo
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Renata Moreno
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
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6
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Corneloup A, Caumont-Sarcos A, Kamgoue A, Marty B, Le PTN, Siguier P, Guynet C, Ton-Hoang B. TnpAREP and REP sequences dissemination in bacterial genomes: REP recognition determinants. Nucleic Acids Res 2021; 49:6982-6995. [PMID: 34161591 PMCID: PMC8266576 DOI: 10.1093/nar/gkab524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 05/27/2021] [Accepted: 06/17/2021] [Indexed: 11/12/2022] Open
Abstract
REP, diverse palindromic DNA sequences found at high copy number in many bacterial genomes, have been attributed important roles in cell physiology but their dissemination mechanisms are poorly understood. They might represent non-autonomous transposable elements mobilizable by TnpAREP, the first prokaryotic domesticated transposase associated with REP. TnpAREP, fundamentally different from classical transposases, are members of the HuH superfamily and closely related to the transposases of the IS200/IS605 family. We previously showed that Escherichia coli TnpAREP processes cognate single stranded REP in vitro and that this activity requires the integrity of the REP structure, in particular imperfect palindromes interrupted by a bulge and preceded by a conserved DNA motif. A second group of REPs rather carry perfect palindromes, raising questions about how the latter are recognized by their cognate TnpAREP. To get insight into the importance of REP structural and sequence determinants in these two groups, we developed an in vitro activity assay coupled to a mutational analysis for three different TnpAREP/REP duos via a SELEX approach. We also tackled the question of how the cleavage site is selected. This study revealed that two TnpAREP groups have co-evolved with their cognate REPs and use different strategies to recognize their REP substrates.
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Affiliation(s)
- Alix Corneloup
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), CBI, CNRS, Université Toulouse UPS, Toulouse, France
| | - Anne Caumont-Sarcos
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), CBI, CNRS, Université Toulouse UPS, Toulouse, France
| | | | - Brigitte Marty
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), CBI, CNRS, Université Toulouse UPS, Toulouse, France
| | - Phan Thai Nguyen Le
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), CBI, CNRS, Université Toulouse UPS, Toulouse, France
| | - Patricia Siguier
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), CBI, CNRS, Université Toulouse UPS, Toulouse, France
| | - Catherine Guynet
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), CBI, CNRS, Université Toulouse UPS, Toulouse, France
| | - Bao Ton-Hoang
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), CBI, CNRS, Université Toulouse UPS, Toulouse, France
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7
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Hibernation-Promoting Factor Sequesters Staphylococcus aureus Ribosomes to Antagonize RNase R-Mediated Nucleolytic Degradation. mBio 2021; 12:e0033421. [PMID: 34253058 PMCID: PMC8406268 DOI: 10.1128/mbio.00334-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Bacterial and eukaryotic hibernation factors prevent translation by physically blocking the decoding center of ribosomes, a phenomenon called ribosome hibernation that often occurs in response to nutrient deprivation. The human pathogen Staphylococcus aureus lacking the sole hibernation factor HPF undergoes massive ribosome degradation via an unknown pathway. Using genetic and biochemical approaches, we find that inactivating the 3′-to-5′ exonuclease RNase R suppresses ribosome degradation in the Δhpf mutant. In vitro cell-free degradation assays confirm that 30S and 70S ribosomes isolated from the Δhpf mutant are extremely susceptible to RNase R, in stark contrast to nucleolytic resistance of the HPF-bound 70S and 100S complexes isolated from the wild type. In the absence of HPF, specific S. aureus 16S rRNA helices are sensitive to nucleolytic cleavage. These RNase hot spots are distinct from that found in the Escherichia coli ribosomes. S. aureus RNase R is associated with ribosomes, but unlike the E. coli counterpart, it is not regulated by general stressors and acetylation. The results not only highlight key differences between the evolutionarily conserved RNase R homologs but also provide direct evidence that HPF preserves ribosome integrity beyond its role in translational avoidance, thereby poising the hibernating ribosomes for rapid resumption of translation.
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8
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Chen X, Lu Y. In silico Design of Linear DNA for Robust Cell-Free Gene Expression. Front Bioeng Biotechnol 2021; 9:670341. [PMID: 34095101 PMCID: PMC8169995 DOI: 10.3389/fbioe.2021.670341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/06/2021] [Indexed: 12/25/2022] Open
Abstract
Cell-free gene expression systems with linear DNA expression templates (LDETs) have been widely applied in artificial cells, biochips, and high-throughput screening. However, due to the degradation caused by native nucleases in cell extracts, the transcription with linear DNA templates is weak, thereby resulting in low protein expression level, which greatly limits the development of cell-free systems using linear DNA templates. In this study, the protective sequences for stabilizing linear DNA and the transcribed mRNAs were rationally designed according to nucleases' action mechanism, whose effectiveness was evaluated through computer simulation and cell-free gene expression. The cell-free experiment results indicated that, with the combined protection of designed sequence and GamS protein, the protein expression of LDET-based cell-free systems could reach the same level as plasmid-based cell-free systems. This study would potentially promote the development of the LDET-based cell-free gene expression system for broader applications.
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Affiliation(s)
- Xinjie Chen
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
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9
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Mfd regulates RNA polymerase association with hard-to-transcribe regions in vivo, especially those with structured RNAs. Proc Natl Acad Sci U S A 2021; 118:2008498118. [PMID: 33443179 DOI: 10.1073/pnas.2008498118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
RNA polymerase (RNAP) encounters various roadblocks during transcription. These obstacles can impede RNAP movement and influence transcription, ultimately necessitating the activity of RNAP-associated factors. One such factor is the bacterial protein Mfd, a highly conserved DNA translocase and evolvability factor that interacts with RNAP. Although Mfd is thought to function primarily in the repair of DNA lesions that stall RNAP, increasing evidence suggests that it may also be important for transcription regulation. However, this is yet to be fully characterized. To shed light on Mfd's in vivo functions, we identified the chromosomal regions where it associates. We analyzed Mfd's impact on RNAP association and transcription regulation genome-wide. We found that Mfd represses RNAP association at many chromosomal regions. We found that these regions show increased RNAP pausing, suggesting that they are hard to transcribe. Interestingly, we noticed that the majority of the regions where Mfd regulates transcription contain highly structured regulatory RNAs. The RNAs identified regulate a myriad of biological processes, ranging from metabolism to transfer RNA regulation to toxin-antitoxin (TA) functions. We found that cells lacking Mfd are highly sensitive to toxin overexpression. Finally, we found that Mfd promotes mutagenesis in at least one toxin gene, suggesting that its function in regulating transcription may promote evolution of certain TA systems and other regions containing strong RNA secondary structures. We conclude that Mfd is an RNAP cofactor that is important, and at times critical, for transcription regulation at hard-to-transcribe regions, especially those that express structured regulatory RNAs.
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Park HJ, Gokhale CS, Bertels F. How sequence populations persist inside bacterial genomes. Genetics 2021; 217:6151697. [PMID: 33724360 PMCID: PMC8049555 DOI: 10.1093/genetics/iyab027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/04/2021] [Indexed: 01/04/2023] Open
Abstract
Compared to their eukaryotic counterparts, bacterial genomes are small and contain extremely tightly packed genes. Repetitive sequences are rare but not completely absent. One of the most common repeat families is REPINs. REPINs can replicate in the host genome and form populations that persist for millions of years. Here, we model the interactions of these intragenomic sequence populations with the bacterial host. We first confirm well-established results, in the presence and absence of horizontal gene transfer (hgt) sequence populations either expand until they drive the host to extinction or the sequence population gets purged from the genome. We then show that a sequence population can be stably maintained, when each individual sequence provides a benefit that decreases with increasing sequence population size. Maintaining a sequence population of stable size also requires the replication of the sequence population to be costly to the host, otherwise the sequence population size will increase indefinitely. Surprisingly, in regimes with high hgt rates, the benefit conferred by the sequence population does not have to exceed the damage it causes to its host. Our analyses provide a plausible scenario for the persistence of sequence populations in bacterial genomes. We also hypothesize a limited biologically relevant parameter range for the provided benefit, which can be tested in future experiments.
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Affiliation(s)
- Hye Jin Park
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany.,Asia Pacific Center for Theoretical Physics, Pohang, 37673, Korea.,Department of Physics, POSTECH, Pohang, 37673, Korea
| | - Chaitanya S Gokhale
- Research Group for Theoretical Models of Eco-evolutionary Dynamics, Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany
| | - Frederic Bertels
- Research Group for Microbial Molecular Evolution, Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany
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11
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Kiselev S, Markelova N, Masulis I. Divergently Transcribed ncRNAs in Escherichia coli: Refinement of the Transcription Starts Assumes Functional Diversification. Front Mol Biosci 2021; 8:610453. [PMID: 33748186 PMCID: PMC7967276 DOI: 10.3389/fmolb.2021.610453] [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: 09/25/2020] [Accepted: 01/07/2021] [Indexed: 02/05/2023] Open
Abstract
Non-coding regulatory RNAs (ncRNAs) comprise specialized group of essential genetically encoded biological molecules involved in the wide variety of cellular metabolic processes. The progressive increase in the number of newly identified ncRNAs and the defining of their genome location indicate their predominant nesting in intergenic regions and expression under the control of their own regulatory elements. At the same time, the regulation of ncRNA's transcription cannot be considered in isolation from the processes occurring in the immediate genetic environment. A number of experimental data indicate the notable impact of positional regulation of gene expression mediated by dynamic temporal DNA rearrangements accompanying transcription events in the vicinity of neighboring genes. This issue can be perceived as particularly significant for divergently transcribed ncRNAs being actually subjected to double regulatory pressure. Based on available results of RNAseq experiments for Escherichia coli, we screened out divergent ncRNAs and the adjacent genes for the exact positions of transcription start sites (TSSs) and relative efficiency of RNA production. This analysis revealed extension or shortening of some previously annotated ncRNAs resulting in modified secondary structure, confirmed stable expression of four ncRNAs annotated earlier as putative, and approved the possibility of expression of divergently transcribed ncRNAs containing repetitive extragenic palindromic (REP) elements. The biogenesis of secreted ncRNAs from divergently transcribed ffs, chiX, ralA, and ryhB is discussed taking into account positions of TSSs. Refinement of TSSs for the neighboring genes renders some ncRNAs as true antisense overlapping with 5'UTR of divergently transcribed mRNAs.
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12
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Ribosome collisions alter frameshifting at translational reprogramming motifs in bacterial mRNAs. Proc Natl Acad Sci U S A 2019; 116:21769-21779. [PMID: 31591196 PMCID: PMC6815119 DOI: 10.1073/pnas.1910613116] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ribosomes move along mRNAs in 3-nucleotide steps as they interpret codons that specify which amino acid is required at each position in the protein. There are multiple examples of genes with DNA sequences that do not match the produced proteins because ribosomes move to a new reading frame in the message before finishing translation (so-called frameshifting). This report shows that, when ribosomes stall at mRNA regions prone to cause frameshifting events, trailing ribosomes that collide with them can significantly change the outcome and potentially regulate protein production. This work highlights the principle that biological macromolecules do not function in isolation, and it provides an example of how physical interactions between neighboring complexes can be used to augment their performance. Translational frameshifting involves the repositioning of ribosomes on their messages into decoding frames that differ from those dictated during initiation. Some messenger RNAs (mRNAs) contain motifs that promote deliberate frameshifting to regulate production of the encoded proteins. The mechanisms of frameshifting have been investigated in many systems, and the resulting models generally involve single ribosomes responding to stimulator sequences in their engaged mRNAs. We discovered that the abundance of ribosomes on messages containing the IS3, dnaX, and prfB frameshift motifs significantly influences the levels of frameshifting. We show that this phenomenon results from ribosome collisions that occur during translational stalling, which can alter frameshifting in both the stalled and trailing ribosomes. Bacteria missing ribosomal protein bL9 are known to exhibit a reduction in reading frame maintenance and to have a strong dependence on elongation factor P (EFP). We discovered that ribosomes lacking bL9 become compacted closer together during collisions and that the E-sites of the stalled ribosomes appear to become blocked, which suggests subsequent transpeptidation in transiently stalled ribosomes may become compromised in the absence of bL9. In addition, we determined that bL9 can suppress frameshifting of its host ribosome, likely by regulating E-site dynamics. These findings provide mechanistic insight into the behavior of colliding ribosomes during translation and suggest naturally occurring frameshift elements may be regulated by the abundance of ribosomes relative to an mRNA pool.
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13
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Rousset F, Cui L, Siouve E, Becavin C, Depardieu F, Bikard D. Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors. PLoS Genet 2018; 14:e1007749. [PMID: 30403660 PMCID: PMC6242692 DOI: 10.1371/journal.pgen.1007749] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 11/19/2018] [Accepted: 10/09/2018] [Indexed: 12/22/2022] Open
Abstract
High-throughput genetic screens are powerful methods to identify genes linked to a given phenotype. The catalytic null mutant of the Cas9 RNA-guided nuclease (dCas9) can be conveniently used to silence genes of interest in a method also known as CRISPRi. Here, we report a genome-wide CRISPR-dCas9 screen using a starting pool of ~ 92,000 sgRNAs which target random positions in the chromosome of E. coli. To benchmark our method, we first investigate its utility to predict gene essentiality in the genome of E. coli during growth in rich medium. We could identify 79% of the genes previously reported as essential and demonstrate the non-essentiality of some genes annotated as essential. In addition, we took advantage of the intermediate repression levels obtained when targeting the template strand of genes to show that cells are very sensitive to the expression level of a limited set of essential genes. Our data can be visualized on CRISPRbrowser, a custom web interface available at crispr.pasteur.fr. We then apply the screen to discover E. coli genes required by phages λ, T4 and 186 to kill their host, highlighting the involvement of diverse host pathways in the infection process of the three tested phages. We also identify colanic acid capsule synthesis as a shared resistance mechanism to all three phages. Finally, using a plasmid packaging system and a transduction assay, we identify genes required for the formation of functional λ capsids, thus covering the entire phage cycle. This study demonstrates the usefulness and convenience of pooled genome-wide CRISPR-dCas9 screens in bacteria and paves the way for their broader use as a powerful tool in bacterial genomics. Over the past few years, CRISPR-Cas technologies have emerged as powerful tools to edit genomes and modulate gene expression. They have been applied to perform high-throughput genetic screens with the purpose to understand the function of genes in a systematic manner, but the application of these screens to bacteria have so far remained limited. Here, we present the use of a library of ~92,000 guide RNAs directing the dCas9 protein to silence one by one all the genes in the chromosome of E. coli. To benchmark our method, we first investigate the performance of the technique to identify essential genes, highlighting several non-essential genes also found to be essential by other methods. We then apply our method to detect bacterial genes required by three different bacteriophages to kill E. coli and for the production of functional progeny by phage λ. Our screens highlight previously known and new genetic interactions between phages and their host’s pathways and emphasize the importance of bacterial capsule in the resistance to multiple phages. Altogether, our results demonstrate the usefulness of genome-wide CRISPR-dCas9 screens in bacteria to uncover genes involved in various phenotypes.
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Affiliation(s)
- François Rousset
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Lun Cui
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
| | - Elise Siouve
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
| | - Christophe Becavin
- Hub Bioinformatique et Biostatistique, Institut Pasteur - C3BI, USR 3756 IP CNRS, Paris, France
| | - Florence Depardieu
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
| | - David Bikard
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
- * E-mail:
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14
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Deng C, Lv X, Li J, Liu Y, Du G, Amaro RL, Liu L. Synthetic repetitive extragenic palindromic (REP) sequence as an efficient mRNA stabilizer for protein production and metabolic engineering in prokaryotic cells. Biotechnol Bioeng 2018; 116:5-18. [DOI: 10.1002/bit.26841] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/24/2018] [Accepted: 09/14/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Chen Deng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
- Key Laboratory of Industrial Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
- Key Laboratory of Industrial Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
| | - Jianghua Li
- Key Laboratory of Industrial Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
- Key Laboratory of Industrial Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
| | | | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
- Key Laboratory of Industrial Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
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15
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Quentin Y, Siguier P, Chandler M, Fichant G. Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases. BMC Genomics 2018; 19:475. [PMID: 29914351 PMCID: PMC6006769 DOI: 10.1186/s12864-018-4836-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/29/2018] [Indexed: 12/11/2022] Open
Abstract
Background Some mobile genetic elements target the lagging strand template during DNA replication. Bacterial examples are insertion sequences IS608 and ISDra2 (IS200/IS605 family members). They use obligatory single-stranded circular DNA intermediates for excision and insertion and encode a transposase, TnpAIS200, which recognizes subterminal secondary structures at the insertion sequence ends. Similar secondary structures, Repeated Extragenic Palindromes (REP), are present in many bacterial genomes. TnpAIS200-related proteins, TnpAREP, have been identified and could be responsible for REP sequence proliferation. These proteins share a conserved HuH/Tyrosine core domain responsible for catalysis and are involved in processes of ssDNA cleavage and ligation. Our goal is to characterize the diversity of these proteins collectively referred as the TnpAY1 family. Results A genome-wide analysis of sequences similar to TnpAIS200 and TnpAREP in prokaryotes revealed a large number of family members with a wide taxonomic distribution. These can be arranged into three distinct classes and 12 subclasses based on sequence similarity. One subclass includes sequences similar to TnpAIS200. Proteins from other subclasses are not associated with typical insertion sequence features. These are characterized by specific additional domains possibly involved in protein/DNA or protein/protein interactions. Their genes are found in more than 25% of species analyzed. They exhibit a patchy taxonomic distribution consistent with dissemination by horizontal gene transfers followed by loss. The tnpAREP genes of five subclasses are flanked by typical REP sequences in a REPtron-like arrangement. Four distinct REP types were characterized with a subclass specific distribution. Other subclasses are not associated with REP sequences but have a large conserved domain located in C-terminal end of their sequence. This unexpected diversity suggests that, while most likely involved in processing single-strand DNA, proteins from different subfamilies may play a number of different roles. Conclusions We established a detailed classification of TnpAY1 proteins, consolidated by the analysis of the conserved core domains and the characterization of additional domains. The data obtained illustrate the unexpected diversity of the TnpAY1 family and provide a strong framework for future evolutionary and functional studies. By their potential function in ssDNA editing, they may confer adaptive responses to host cell physiology and metabolism. Electronic supplementary material The online version of this article (10.1186/s12864-018-4836-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yves Quentin
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France.
| | - Patricia Siguier
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France
| | - Mick Chandler
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France.
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France
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16
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Bertels F, Gallie J, Rainey PB. Identification and Characterization of Domesticated Bacterial Transposases. Genome Biol Evol 2017; 9:2110-2121. [PMID: 28910967 PMCID: PMC5581495 DOI: 10.1093/gbe/evx146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2017] [Indexed: 12/26/2022] Open
Abstract
Selfish genetic elements, such as insertion sequences and transposons are found in most genomes. Transposons are usually identifiable by their high copy number within genomes. In contrast, REP-associated tyrosine transposases (RAYTs), a recently described class of bacterial transposase, are typically present at just one copy per genome. This suggests that RAYTs no longer copy themselves and thus they no longer function as a typical transposase. Motivated by this possibility we interrogated thousands of fully sequenced bacterial genomes in order to determine patterns of RAYT diversity, their distribution across chromosomes and accessory elements, and rate of duplication. RAYTs encompass exceptional diversity and are divisible into at least five distinct groups. They possess features more similar to housekeeping genes than insertion sequences, are predominantly vertically transmitted and have persisted through evolutionary time to the point where they are now found in 24% of all species for which at least one fully sequenced genome is available. Overall, the genomic distribution of RAYTs suggests that they have been coopted by host genomes to perform a function that benefits the host cell.
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Affiliation(s)
- Frederic Bertels
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, New Zealand.,Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jenna Gallie
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, New Zealand.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Laboratoire de Génétique de l'Evolution, Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), PSL Research University, Paris, France
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17
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Bertels F, Gokhale CS, Traulsen A. Discovering Complete Quasispecies in Bacterial Genomes. Genetics 2017; 206:2149-2157. [PMID: 28630115 PMCID: PMC5560812 DOI: 10.1534/genetics.117.201160] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 06/08/2017] [Indexed: 01/15/2023] Open
Abstract
Mobile genetic elements can be found in almost all genomes. Possibly the most common nonautonomous mobile genetic elements in bacteria are repetitive extragenic palindromic doublets forming hairpins (REPINs) that can occur hundreds of times within a genome. The sum of all REPINs in a genome can be viewed as an evolving population because REPINs replicate and mutate. In contrast to most other biological populations, we know the exact composition of the REPIN population and the sequence of each member of the population. Here, we model the evolution of REPINs as quasispecies. We fit our quasispecies model to 10 different REPIN populations from 10 different bacterial strains and estimate effective duplication rates. Our estimated duplication rates range from ∼5 × 10-9 to 15 × 10-9 duplications per bacterial generation per REPIN. The small range and the low level of the REPIN duplication rates suggest a universal trade-off between the survival of the REPIN population and the reduction of the mutational load for the host genome. The REPIN populations we investigated also possess features typical of other natural populations. One population shows hallmarks of a population that is going extinct, another population seems to be growing in size, and we also see an example of competition between two REPIN populations.
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Affiliation(s)
- Frederic Bertels
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Chaitanya S Gokhale
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Arne Traulsen
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
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18
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Global analysis of protein lysine succinylation profiles in common wheat. BMC Genomics 2017; 18:309. [PMID: 28427325 PMCID: PMC5397794 DOI: 10.1186/s12864-017-3698-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 04/11/2017] [Indexed: 12/21/2022] Open
Abstract
Background Protein lysine succinylation is an important post-translational modification and plays a critical regulatory role in almost every aspects of cell metabolism in both eukaryotes and prokaryotes. Common wheat is one of the major global cereal crops. However, to date, little is known about the functions of lysine succinylation in this plant. Here, we performed a global analysis of lysine succinylation in wheat and examined its overlap with lysine acetylation. Results In total, 330 lysine succinylated modification sites were identified in 173 proteins. Bioinformatics analysis showed that the modified proteins are distributed in multiple subcellular compartments and are involved in a wide variety of biological processes such as photosynthesis and the Calvin-Benson cycle, suggesting an important role for lysine succinylation in these processes. Five putative succinylation motifs were identified. A protein interaction network analysis revealed that diverse interactions are modulated by protein succinylation. Moreover, 21 succinyl-lysine sites were found to be acetylated at the same position, and 33 proteins were modified by both acetylation and succinylation, suggesting an extensive overlap between succinylation and acetylation in common wheat. Comparative analysis indicated that lysine succinylation is conserved between common wheat and Brachypodium distachyon. Conclusions These results suggest that lysine succinylation is involved in diverse biological processes, especially in photosynthesis and carbon fixation. This systematic analysis represents the first global analysis of lysine succinylation in common wheat and provides an important resource for exploring the physiological role of lysine succinylation in this cereal crop and likely in all plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3698-2) contains supplementary material, which is available to authorized users.
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19
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Hahn J, Thalmann S, Migur A, von Boeselager RF, Kubatova N, Kubareva E, Schwalbe H, Evguenieva-Hackenberg E. Conserved small mRNA with an unique, extended Shine-Dalgarno sequence. RNA Biol 2016; 14:1353-1363. [PMID: 27834614 PMCID: PMC5711450 DOI: 10.1080/15476286.2016.1256534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Up to now, very small protein-coding genes have remained unrecognized in sequenced genomes. We identified an mRNA of 165 nucleotides (nt), which is conserved in Bradyrhizobiaceae and encodes a polypeptide with 14 amino acid residues (aa). The small mRNA harboring a unique Shine-Dalgarno sequence (SD) with a length of 17 nt was localized predominantly in the ribosome-containing P100 fraction of Bradyrhizobium japonicum USDA 110. Strong interaction between the mRNA and 30S ribosomal subunits was demonstrated by their co-sedimentation in sucrose density gradient. Using translational fusions with egfp, we detected weak translation and found that it is impeded by both the extended SD and the GTG start codon (instead of ATG). Biophysical characterization (CD- and NMR-spectroscopy) showed that synthesized polypeptide remained unstructured in physiological puffer. Replacement of the start codon by a stop codon increased the stability of the transcript, strongly suggesting additional posttranscriptional regulation at the ribosome. Therefore, the small gene was named rreB (ribosome-regulated expression in Bradyrhizobiaceae). Assuming that the unique ribosome binding site (RBS) is a hallmark of rreB homologs or similarly regulated genes, we looked for similar putative RBS in bacterial genomes and detected regions with at least 16 nt complementarity to the 3′-end of 16S rRNA upstream of sORFs in Caulobacterales, Rhizobiales, Rhodobacterales and Rhodospirillales. In the Rhodobacter/Roseobacter lineage of α-proteobacteria the corresponding gene (rreR) is conserved and encodes an 18 aa protein. This shows how specific RBS features can be used to identify new genes with presumably similar control of expression at the RNA level.
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Affiliation(s)
- Julia Hahn
- a Institute of Microbiology and Molecular Biology, Justus-Liebig-University , Gießen , Germany
| | - Sebastian Thalmann
- a Institute of Microbiology and Molecular Biology, Justus-Liebig-University , Gießen , Germany
| | - Anzhela Migur
- a Institute of Microbiology and Molecular Biology, Justus-Liebig-University , Gießen , Germany.,b A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University , Leninskye Gory 1, Moscow , Russia
| | | | - Nina Kubatova
- d Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität , Frankfurt am Main , Germany
| | - Elena Kubareva
- b A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University , Leninskye Gory 1, Moscow , Russia
| | - Harald Schwalbe
- d Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität , Frankfurt am Main , Germany
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20
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Hahn J, Tsoy OV, Thalmann S, Čuklina J, Gelfand MS, Evguenieva-Hackenberg E. Small Open Reading Frames, Non-Coding RNAs and Repetitive Elements in Bradyrhizobium japonicum USDA 110. PLoS One 2016; 11:e0165429. [PMID: 27788207 PMCID: PMC5082802 DOI: 10.1371/journal.pone.0165429] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 10/11/2016] [Indexed: 11/18/2022] Open
Abstract
Small open reading frames (sORFs) and genes for non-coding RNAs are poorly investigated components of most genomes. Our analysis of 1391 ORFs recently annotated in the soybean symbiont Bradyrhizobium japonicum USDA 110 revealed that 78% of them contain less than 80 codons. Twenty-one of these sORFs are conserved in or outside Alphaproteobacteria and most of them are similar to genes found in transposable elements, in line with their broad distribution. Stabilizing selection was demonstrated for sORFs with proteomic evidence and bll1319_ISGA which is conserved at the nucleotide level in 16 alphaproteobacterial species, 79 species from other taxa and 49 other Proteobacteria. Further we used Northern blot hybridization to validate ten small RNAs (BjsR1 to BjsR10) belonging to new RNA families. We found that BjsR1 and BjsR3 have homologs outside the genus Bradyrhizobium, and BjsR5, BjsR6, BjsR7, and BjsR10 have up to four imperfect copies in Bradyrhizobium genomes. BjsR8, BjsR9, and BjsR10 are present exclusively in nodules, while the other sRNAs are also expressed in liquid cultures. We also found that the level of BjsR4 decreases after exposure to tellurite and iron, and this down-regulation contributes to survival under high iron conditions. Analysis of additional small RNAs overlapping with 3’-UTRs revealed two new repetitive elements named Br-REP1 and Br-REP2. These REP elements may play roles in the genomic plasticity and gene regulation and could be useful for strain identification by PCR-fingerprinting. Furthermore, we studied two potential toxin genes in the symbiotic island and confirmed toxicity of the yhaV homolog bll1687 but not of the newly annotated higB homolog blr0229_ISGA in E. coli. Finally, we revealed transcription interference resulting in an antisense RNA complementary to blr1853, a gene induced in symbiosis. The presented results expand our knowledge on sORFs, non-coding RNAs and repetitive elements in B. japonicum and related bacteria.
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Affiliation(s)
- Julia Hahn
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
| | - Olga V. Tsoy
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny Ln. 19, Moscow, 127051, Russia
| | - Sebastian Thalmann
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
| | - Jelena Čuklina
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny Ln. 19, Moscow, 127051, Russia
- ETH, Institute of Molecular Systems Biology, Zürich, Switzerland
| | - Mikhail S. Gelfand
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny Ln. 19, Moscow, 127051, Russia
- Skolkovo Institute of Science and Technology, Nobel Str. 3, Moscow, 143026, Russia
- Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Vorobyevy Gory 1–73, Moscow, 119234, Russia
- Faculty of Computer Science, Higher School of Economics, Kochnovsky Dr. 3, Moscow, 125319, Russia
- * E-mail: (EEH); (MSG)
| | - Elena Evguenieva-Hackenberg
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
- * E-mail: (EEH); (MSG)
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Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV. Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res 2016; 44:7007-78. [PMID: 27436286 PMCID: PMC5009743 DOI: 10.1093/nar/gkw530] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/26/2016] [Indexed: 12/15/2022] Open
Abstract
Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.
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Affiliation(s)
- John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland School of Microbiology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pramod R Bhatt
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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Briani F, Carzaniga T, Dehò G. Regulation and functions of bacterial PNPase. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:241-58. [PMID: 26750178 DOI: 10.1002/wrna.1328] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/23/2015] [Accepted: 11/23/2015] [Indexed: 01/29/2023]
Abstract
Polynucleotide phosphorylase (PNPase) is an exoribonuclease that catalyzes the processive phosphorolytic degradation of RNA from the 3'-end. The enzyme catalyzes also the reverse reaction of polymerization of nucleoside diphosphates that has been implicated in the generation of heteropolymeric tails at the RNA 3'-end. The enzyme is widely conserved and plays a major role in RNA decay in both Gram-negative and Gram-positive bacteria. Moreover, it participates in maturation and quality control of stable RNA. PNPase autoregulates its own expression at post-transcriptional level through a complex mechanism that involves the endoribonuclease RNase III and translation control. The activity of PNPase is modulated in an intricate and still unclear manner by interactions with small molecules and recruitment in different multiprotein complexes. Not surprisingly, given the wide spectrum of PNPase substrates, PNPase-defective mutations in different bacterial species have pleiotropic effects and perturb the execution of genetic programs involving drastic changes in global gene expression such as biofilm formation, growth at suboptimal temperatures, and virulence.
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Affiliation(s)
- Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Thomas Carzaniga
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Gianni Dehò
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
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Abstract
Repetitive Extragenic Palindromic (REP) sequences are highly conserved, structured, 35- to 40-nt elements located at ∼500 positions around the Escherichia coli chromosome. They are found in intergenic regions and are transcribed together with their upstream genes. Although their stable stem-loop structures protect messages against exoribonuclease digestion, their primary function has remained unknown. Recently, we found that about half of all REP sequences have the potential to stall ribosomes immediately upstream of the termination codon, leading to endonucleolytic cleavage of the mRNA, and induction of the trans-translation process. As a consequence, the mRNA and almost completed protein are degraded, and protein production from the affected gene is down-regulated. The process is critically dependent on the location of the REP element, with an effect only if it is within 15 nt of the termination codon. Using nrdAB as a model, we found that its down-regulation is affected by RNA helicases. Elimination of 6 helicases lowered NrdA production further, whereas overexpression of any RNA helicase partially reversed the downregulation. UV stress completely reversed down-regulation of NrdA production. Analysis of genes containing a REP sequence within 15 nt of the termination codon revealed that most, if not all, are up-regulated by environmental stress, as are RNA helicases. Based on these findings, we propose that REP-dependent downregulation serves as a mechanism to allow a rapid response to environmental stresses whereby RNA helicases partially open the REP elements enabling ribosomes to complete translation immediately increasing protein production from the affected genes.
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Affiliation(s)
- Wenxing Liang
- a The Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University , Qingdao , China
| | - Murray P Deutscher
- b Department of Biochemistry and Molecular Biology , Miller School of Medicine, University of Miami , Miami , Florida , USA
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Kotini SB, Peske F, Rodnina MV. Partitioning between recoding and termination at a stop codon-selenocysteine insertion sequence. Nucleic Acids Res 2015; 43:6426-38. [PMID: 26040702 PMCID: PMC4513850 DOI: 10.1093/nar/gkv558] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 05/14/2015] [Accepted: 05/17/2015] [Indexed: 11/13/2022] Open
Abstract
Selenocysteine (Sec) is inserted into proteins by recoding a UGA stop codon followed by a selenocysteine insertion sequence (SECIS). UGA recoding by the Sec machinery is believed to be very inefficient owing to RF2-mediated termination at UGA. Here we show that recoding efficiency in vivo is 30-40% independently of the cell growth rate. Efficient recoding requires sufficient selenium concentrations in the medium. RF2 is an unexpectedly poor competitor of Sec. We recapitulate the major characteristics of SECIS-dependent UGA recoding in vitro using a fragment of fdhF-mRNA encoding a natural bacterial selenoprotein. Only 40% of actively translating ribosomes that reach the UGA codon insert Sec, even in the absence of RF2, suggesting that the capacity to insert Sec into proteins is inherently limited. RF2 does not compete with the Sec incorporation machinery; rather, it terminates translation on those ribosomes that failed to incorporate Sec. The data suggest a model in which early recruitment of Sec-tRNA(Sec)-SelB-GTP to the SECIS blocks the access of RF2 to the stop codon, thereby prioritizing recoding over termination at Sec-dedicated stop codons.
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Affiliation(s)
- Suresh Babu Kotini
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
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