Pub Date : 2022-02-23DOI: 10.1186/s13100-022-00262-6
Blair G Paul, A Murat Eren
Since the first discovery of reverse transcriptase in bacteria, and later in archaea, bacterial and archaeal retroelements have been defined by their common enzyme that coordinates diverse functions. Yet, evolutionary refinement has produced distinct retroelements across the tree of microbial life that are perhaps best described in terms of their programmed RNA-a compact sequence that preserves core information for a sophisticated mechanism. From this perspective, reverse transcriptase has been selected as the modular tool for carrying out nature's instructions in various RNA templates. Beneficial retroelements-those that can provide a fitness advantage to their host-evolved to their extant forms in a wide array of microorganisms and their viruses, spanning nearly all habitats. Within each specialized retroelement class, several universal features seem to be shared across diverse taxa, while specific functional and mechanistic insights are based on only a few model retroelement systems from clinical isolates. Currently, little is known about the diversity of cellular functions and ecological significance of retroelements across different biomes. With increasing availability of isolate, metagenome-assembled, and single-amplified genomes, the taxonomic and functional breadth of prokaryotic retroelements is coming into clearer view. This review explores the recently characterized classes of beneficial, yet accessory retroelements of bacteria and archaea. We describe how these specialized mechanisms exploit a form of fixed mobility, whereby the retroelements do not appear to proliferate selfishly throughout the genome. Moreover, we discuss computational approaches for systematic identification of retroelements from vast sequence repositories and highlight recent discoveries in terms of their apparent distribution and ecological significance in nature. Lastly, we present a new perspective on the eco-evolutionary significance of these genetic elements in marine bacteria and demonstrate approaches that enable the characterization of their environmental diversity through metagenomics.
{"title":"Eco-evolutionary significance of domesticated retroelements in microbial genomes.","authors":"Blair G Paul, A Murat Eren","doi":"10.1186/s13100-022-00262-6","DOIUrl":"10.1186/s13100-022-00262-6","url":null,"abstract":"<p><p>Since the first discovery of reverse transcriptase in bacteria, and later in archaea, bacterial and archaeal retroelements have been defined by their common enzyme that coordinates diverse functions. Yet, evolutionary refinement has produced distinct retroelements across the tree of microbial life that are perhaps best described in terms of their programmed RNA-a compact sequence that preserves core information for a sophisticated mechanism. From this perspective, reverse transcriptase has been selected as the modular tool for carrying out nature's instructions in various RNA templates. Beneficial retroelements-those that can provide a fitness advantage to their host-evolved to their extant forms in a wide array of microorganisms and their viruses, spanning nearly all habitats. Within each specialized retroelement class, several universal features seem to be shared across diverse taxa, while specific functional and mechanistic insights are based on only a few model retroelement systems from clinical isolates. Currently, little is known about the diversity of cellular functions and ecological significance of retroelements across different biomes. With increasing availability of isolate, metagenome-assembled, and single-amplified genomes, the taxonomic and functional breadth of prokaryotic retroelements is coming into clearer view. This review explores the recently characterized classes of beneficial, yet accessory retroelements of bacteria and archaea. We describe how these specialized mechanisms exploit a form of fixed mobility, whereby the retroelements do not appear to proliferate selfishly throughout the genome. Moreover, we discuss computational approaches for systematic identification of retroelements from vast sequence repositories and highlight recent discoveries in terms of their apparent distribution and ecological significance in nature. Lastly, we present a new perspective on the eco-evolutionary significance of these genetic elements in marine bacteria and demonstrate approaches that enable the characterization of their environmental diversity through metagenomics.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2022-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8867640/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39946581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-02-16DOI: 10.1186/s13100-022-00263-5
Tobias Baril, Alexander Hayward
Background: Lepidoptera (butterflies and moths) are an important model system in ecology and evolution. A high-quality chromosomal genome assembly is available for the monarch butterfly (Danaus plexippus), but it lacks an in-depth transposable element (TE) annotation, presenting an opportunity to explore monarch TE dynamics and the impact of TEs on shaping the monarch genome.
Results: We find 6.21% of the monarch genome is comprised of TEs, a reduction of 6.85% compared to the original TE annotation performed on the draft genome assembly. Monarch TE content is low compared to two closely related species with available genomes, Danaus chrysippus (33.97% TE) and Danaus melanippus (11.87% TE). The biggest TE contributions to genome size in the monarch are LINEs and Penelope-like elements, and three newly identified families, r2-hero_dPle (LINE), penelope-1_dPle (Penelope-like), and hase2-1_dPle (SINE), collectively contribute 34.92% of total TE content. We find evidence of recent TE activity, with two novel Tc1 families rapidly expanding over recent timescales (tc1-1_dPle, tc1-2_dPle). LINE fragments show signatures of genomic deletions indicating a high rate of TE turnover. We investigate associations between TEs and wing colouration and immune genes and identify a three-fold increase in TE content around immune genes compared to other host genes.
Conclusions: We provide a detailed TE annotation and analysis for the monarch genome, revealing a considerably smaller TE contribution to genome content compared to two closely related Danaus species with available genome assemblies. We identify highly successful novel DNA TE families rapidly expanding over recent timescales, and ongoing signatures of both TE expansion and removal highlight the dynamic nature of repeat content in the monarch genome. Our findings also suggest that insect immune genes are promising candidates for future interrogation of TE-mediated host adaptation.
背景:鳞翅目昆虫(蝴蝶和飞蛾)是生态学和进化中的重要模式系统。帝王斑蝶(Danaus plexippus)有一个高质量的染色体基因组,但缺乏深入的转座元件(TE)注释,这为探索帝王斑蝶 TE 的动态以及 TE 对帝王斑蝶基因组形成的影响提供了机会:结果:我们发现帝王斑蝶基因组中有 6.21% 由 TE 组成,与对基因组组装草案进行的原始 TE 注释相比减少了 6.85%。与Danaus chrysippus(33.97% TE)和Danaus melanippus(11.87% TE)这两个有可用基因组的近缘物种相比,帝王斑蝶的TE含量较低。帝王斑中对基因组大小贡献最大的 TE 是 LINEs 和 Penelope-like 元素,三个新发现的家族:r2-hero_dPle(LINE)、penelope-1_dPle(Penelope-like)和 hase2-1_dPle(SINE)总共贡献了总 TE 含量的 34.92%。我们发现了近期 TE 活动的证据,两个新的 Tc1 家族(tc1-1_dPle、tc1-2_dPle)在近期迅速扩展。LINE 片段显示出基因组缺失的特征,表明 TE 更替速度很快。我们研究了TE与翅膀着色和免疫基因之间的关联,发现与其他宿主基因相比,免疫基因周围的TE含量增加了三倍:我们对帝王斑鸠基因组进行了详细的 TE 注释和分析,发现与两个有基因组组装的近缘 Danaus 种类相比,TE 对基因组内容的贡献要小得多。我们发现了非常成功的新型 DNA TE 家族,它们在最近的时间尺度内迅速扩展,TE 扩展和移除的持续特征凸显了帝王斑蝶基因组中重复内容的动态性质。我们的发现还表明,昆虫免疫基因是未来研究 TE 介导的宿主适应性的有希望的候选基因。
{"title":"Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus.","authors":"Tobias Baril, Alexander Hayward","doi":"10.1186/s13100-022-00263-5","DOIUrl":"10.1186/s13100-022-00263-5","url":null,"abstract":"<p><strong>Background: </strong>Lepidoptera (butterflies and moths) are an important model system in ecology and evolution. A high-quality chromosomal genome assembly is available for the monarch butterfly (Danaus plexippus), but it lacks an in-depth transposable element (TE) annotation, presenting an opportunity to explore monarch TE dynamics and the impact of TEs on shaping the monarch genome.</p><p><strong>Results: </strong>We find 6.21% of the monarch genome is comprised of TEs, a reduction of 6.85% compared to the original TE annotation performed on the draft genome assembly. Monarch TE content is low compared to two closely related species with available genomes, Danaus chrysippus (33.97% TE) and Danaus melanippus (11.87% TE). The biggest TE contributions to genome size in the monarch are LINEs and Penelope-like elements, and three newly identified families, r2-hero_dPle (LINE), penelope-1_dPle (Penelope-like), and hase2-1_dPle (SINE), collectively contribute 34.92% of total TE content. We find evidence of recent TE activity, with two novel Tc1 families rapidly expanding over recent timescales (tc1-1_dPle, tc1-2_dPle). LINE fragments show signatures of genomic deletions indicating a high rate of TE turnover. We investigate associations between TEs and wing colouration and immune genes and identify a three-fold increase in TE content around immune genes compared to other host genes.</p><p><strong>Conclusions: </strong>We provide a detailed TE annotation and analysis for the monarch genome, revealing a considerably smaller TE contribution to genome content compared to two closely related Danaus species with available genome assemblies. We identify highly successful novel DNA TE families rapidly expanding over recent timescales, and ongoing signatures of both TE expansion and removal highlight the dynamic nature of repeat content in the monarch genome. Our findings also suggest that insect immune genes are promising candidates for future interrogation of TE-mediated host adaptation.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2022-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8848866/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39637536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-02-02DOI: 10.21203/rs.3.rs-1312818/v1
Juan Paolo A. Sicat, Paul Visendi, Steven O. Sewe, S. Bouvaine, S. Seal
Background Whiteflies are agricultural pests that have caused worldwide negative impacts that have led to severe financial losses. The Bemisia tabaci whitefly species complex is the most damaging in terms of their broad crop host range and its ability to serve as vector for over 300 plant viruses. Whitefly genomes of the species complex provide valuable genomic data; however, transposable elements (TEs) within the species complex remain unexplored. This study provides the first accurate exploration of TE content within the B. tabaci species complex.Results This study identified an average of 40.61% of the genomes of three whitefly species (MEAM1, MEDQ, and SSA-ECA) consists of TEs. Majority of the TEs identified were DNA transposons (22.85% average) while SINEs (0.14% average) were the least represented. This study also compared the TE content the three whitefly genomes with three other hemipteran genomes and found a significant difference in the presence of DNA transposons and LINEs. A total of 63 TE superfamilies were identified to be present across the three whitefly species (39 DNA transposons, six LTR, 16 LINE, and two SINE) of which 11 TE superfamilies were identified to not be present in the three other hemipteran genomes (nine DNA transposon, and two LINE). This study is the first to characterize TEs found within different B. tabaci species and has created a standardized annotation workflow that could be used to analyze future whitefly genomes.Conclusion This study is the first to characterize the landscape of TEs within the B. tabaci species complex. The characterization of these elements within the three whitefly genomes shows that TEs occupy a significant portion of the whitefly genome, majority of which are DNA transposons. This study also identified TE superfamilies of note and provides a framework for future TE studies within the species complex.
{"title":"Correction: Characterization of transposable elements within the Bemisia tabaci species complex","authors":"Juan Paolo A. Sicat, Paul Visendi, Steven O. Sewe, S. Bouvaine, S. Seal","doi":"10.21203/rs.3.rs-1312818/v1","DOIUrl":"https://doi.org/10.21203/rs.3.rs-1312818/v1","url":null,"abstract":"\u0000 Background Whiteflies are agricultural pests that have caused worldwide negative impacts that have led to severe financial losses. The Bemisia tabaci whitefly species complex is the most damaging in terms of their broad crop host range and its ability to serve as vector for over 300 plant viruses. Whitefly genomes of the species complex provide valuable genomic data; however, transposable elements (TEs) within the species complex remain unexplored. This study provides the first accurate exploration of TE content within the B. tabaci species complex.Results This study identified an average of 40.61% of the genomes of three whitefly species (MEAM1, MEDQ, and SSA-ECA) consists of TEs. Majority of the TEs identified were DNA transposons (22.85% average) while SINEs (0.14% average) were the least represented. This study also compared the TE content the three whitefly genomes with three other hemipteran genomes and found a significant difference in the presence of DNA transposons and LINEs. A total of 63 TE superfamilies were identified to be present across the three whitefly species (39 DNA transposons, six LTR, 16 LINE, and two SINE) of which 11 TE superfamilies were identified to not be present in the three other hemipteran genomes (nine DNA transposon, and two LINE). This study is the first to characterize TEs found within different B. tabaci species and has created a standardized annotation workflow that could be used to analyze future whitefly genomes.Conclusion This study is the first to characterize the landscape of TEs within the B. tabaci species complex. The characterization of these elements within the three whitefly genomes shows that TEs occupy a significant portion of the whitefly genome, majority of which are DNA transposons. This study also identified TE superfamilies of note and provides a framework for future TE studies within the species complex.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2022-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42717241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-18DOI: 10.1186/s13100-021-00260-0
Alexandra Iouranova, Delphine Grun, Tamara Rossy, Julien Duc, Alexandre Coudray, Michael Imbeault, Jonas de Tribolet-Hardy, Priscilla Turelli, Alexandre Persat, Didier Trono
Background: Transposable element-embedded regulatory sequences (TEeRS) and their KRAB-containing zinc finger protein (KZFP) controllers are increasingly recognized as modulators of gene expression. We aim to characterize the contribution of this system to gene regulation in early human development and germ cells.
Results: Here, after studying genes driven by the long terminal repeat (LTR) of endogenous retroviruses, we identify the ape-restricted ZNF676 as the sequence-specific repressor of a subset of contemporary LTR12 integrants responsible for a large fraction of transpochimeric gene transcripts (TcGTs) generated during human early embryogenesis. We go on to reveal that the binding of this KZFP correlates with the epigenetic marking of these TEeRS in the germline, and is crucial to the control of genes involved in ciliogenesis/flagellogenesis, a biological process that dates back to the last common ancestor of eukaryotes.
Conclusion: These results illustrate how KZFPs and their TE targets contribute to the evolutionary turnover of transcription networks and participate in the transgenerational inheritance of epigenetic traits.
{"title":"KRAB zinc finger protein ZNF676 controls the transcriptional influence of LTR12-related endogenous retrovirus sequences.","authors":"Alexandra Iouranova, Delphine Grun, Tamara Rossy, Julien Duc, Alexandre Coudray, Michael Imbeault, Jonas de Tribolet-Hardy, Priscilla Turelli, Alexandre Persat, Didier Trono","doi":"10.1186/s13100-021-00260-0","DOIUrl":"10.1186/s13100-021-00260-0","url":null,"abstract":"<p><strong>Background: </strong>Transposable element-embedded regulatory sequences (TEeRS) and their KRAB-containing zinc finger protein (KZFP) controllers are increasingly recognized as modulators of gene expression. We aim to characterize the contribution of this system to gene regulation in early human development and germ cells.</p><p><strong>Results: </strong>Here, after studying genes driven by the long terminal repeat (LTR) of endogenous retroviruses, we identify the ape-restricted ZNF676 as the sequence-specific repressor of a subset of contemporary LTR12 integrants responsible for a large fraction of transpochimeric gene transcripts (TcGTs) generated during human early embryogenesis. We go on to reveal that the binding of this KZFP correlates with the epigenetic marking of these TEeRS in the germline, and is crucial to the control of genes involved in ciliogenesis/flagellogenesis, a biological process that dates back to the last common ancestor of eukaryotes.</p><p><strong>Conclusion: </strong>These results illustrate how KZFPs and their TE targets contribute to the evolutionary turnover of transcription networks and participate in the transgenerational inheritance of epigenetic traits.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2022-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8767690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10263436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-13DOI: 10.1186/s13100-022-00261-7
Kenji Ichiyanagi, Kuniaki Saito
The fifth Japanese meeting on host-transposon interactions, titled "Biological Function and Evolution through Interactions between Hosts and Transposable Elements (TEs)," was held online on August 26-27, 2021. The meeting was supported by National Institute of Genetics and aimed to bring together researchers studying the diverse roles of TEs in genome function and evolution, as well as host defense systems against TE mobility by chromatin and RNA modifications and protein-protein interactions. Here, we present the highlights of the talks.
{"title":"The fifth Japanese meeting on biological function and evolution through interactions between hosts and transposable elements.","authors":"Kenji Ichiyanagi, Kuniaki Saito","doi":"10.1186/s13100-022-00261-7","DOIUrl":"https://doi.org/10.1186/s13100-022-00261-7","url":null,"abstract":"<p><p>The fifth Japanese meeting on host-transposon interactions, titled \"Biological Function and Evolution through Interactions between Hosts and Transposable Elements (TEs),\" was held online on August 26-27, 2021. The meeting was supported by National Institute of Genetics and aimed to bring together researchers studying the diverse roles of TEs in genome function and evolution, as well as host defense systems against TE mobility by chromatin and RNA modifications and protein-protein interactions. Here, we present the highlights of the talks.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2022-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8756742/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39932729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-03DOI: 10.1186/s13100-021-00257-9
Ruth M Hall
The insertion sequence IS26 has long been known to play a major role in the recruitment of antibiotic resistance genes into the mobile resistance gene pool of Gram-negative bacteria and IS26 also plays a major role in their subsequent broad dissemination. Related IS, IS431/257 and IS1216 are important in the same roles in Gram positive bacteria. However, until recently the properties of IS26 movement that could potentially explain this ability had not been explored. A much needed insight has come from our recent demonstration that IS26 uses a novel targeted mechanism that is conservative. The targeted conservative mechanism is much more efficient than the known replicative mechanism, which is now more accurately called copy-in. A recent review "The IS6 family, a clinically important group of insertion sequences including IS26" by Varani, He, Siguier, Ross and Chandler published in Mobile DNA has substantially misrepresented the recent studies on the targeted conservative mechanism and at the same time incorrectly implied that any mechanism established for IS26 can be assumed to apply to a range of IS that are at best very distantly related. A few of the most important issues are examined in this comment. Readers are advised to consult the original literature to check facts before drawing firm conclusions.
长期以来,人们都知道插入序列IS26在将抗生素耐药基因招募到革兰氏阴性菌的移动耐药基因库中起着重要作用,IS26在其随后的广泛传播中也起着重要作用。相关IS, IS431/257和IS1216在革兰氏阳性菌中发挥同样重要的作用。然而,直到最近,IS26运动的特性才有可能解释这种能力。我们最近的演示表明,IS26使用了一种新颖的靶向机制,这种机制是保守的。目标保守机制比已知的复制机制更有效,复制机制现在更准确地称为复制-in。最近由Varani, He, Siguier, Ross和Chandler发表在Mobile DNA上的一篇综述“IS6 family, A clinical important group of insertion sequences包括IS26”在很大程度上歪曲了最近关于靶向保守机制的研究,同时错误地暗示为IS26建立的任何机制都可以被认为适用于最多是非常远亲的一系列IS。本文探讨了几个最重要的问题。建议读者在得出确切的结论之前查阅原始文献以核实事实。
{"title":"Comment on \"the IS6 family, a clinically important group of insertion sequences including IS26\" by Varani and co-authors.","authors":"Ruth M Hall","doi":"10.1186/s13100-021-00257-9","DOIUrl":"https://doi.org/10.1186/s13100-021-00257-9","url":null,"abstract":"<p><p>The insertion sequence IS26 has long been known to play a major role in the recruitment of antibiotic resistance genes into the mobile resistance gene pool of Gram-negative bacteria and IS26 also plays a major role in their subsequent broad dissemination. Related IS, IS431/257 and IS1216 are important in the same roles in Gram positive bacteria. However, until recently the properties of IS26 movement that could potentially explain this ability had not been explored. A much needed insight has come from our recent demonstration that IS26 uses a novel targeted mechanism that is conservative. The targeted conservative mechanism is much more efficient than the known replicative mechanism, which is now more accurately called copy-in. A recent review \"The IS6 family, a clinically important group of insertion sequences including IS26\" by Varani, He, Siguier, Ross and Chandler published in Mobile DNA has substantially misrepresented the recent studies on the targeted conservative mechanism and at the same time incorrectly implied that any mechanism established for IS26 can be assumed to apply to a range of IS that are at best very distantly related. A few of the most important issues are examined in this comment. Readers are advised to consult the original literature to check facts before drawing firm conclusions.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2022-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8722046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39659346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-03DOI: 10.1186/s13100-021-00258-8
Alessandro Varani, Susu He, Patricia Siguier, Karen Ross, Michael Chandler
The IS6 family of insertion sequences is a large but coherent group which was originally named to avoid confusion between a number of identical or nearly identical IS that were identified at about the same time and given different names (IS15D, IS26, IS46, IS140, IS160, IS176). The underlying common mechanistic feature of all IS6 family members which have been investigated is that they appear to transpose by replicative transposition and form pseudo compound transposons with the flanking IS in direct repeat and in which associated genes are simply transferred to the target replicon and lost from the donor.In the accompanying letter Hall raises a number of very serious and wide-ranging criticisms of our recent review article concerning the IS6 family of insertion sequences. She clearly feels that we have undervalued her work and that we question or ignore certain of her in vivo results. This impression is almost certainly the result of the standard of proof we generally apply to mechanistic aspects of transposition where we think it important to identify transposition intermediates including the types of synaptic, strand cleavage and strand transfer complexes involved.
{"title":"Response from Varani et al. to \"Comment on 'the IS6 family, a clinically important group of insertion sequences including IS26' by Ruth M. Hall\".","authors":"Alessandro Varani, Susu He, Patricia Siguier, Karen Ross, Michael Chandler","doi":"10.1186/s13100-021-00258-8","DOIUrl":"https://doi.org/10.1186/s13100-021-00258-8","url":null,"abstract":"<p><p>The IS6 family of insertion sequences is a large but coherent group which was originally named to avoid confusion between a number of identical or nearly identical IS that were identified at about the same time and given different names (IS15D, IS26, IS46, IS140, IS160, IS176). The underlying common mechanistic feature of all IS6 family members which have been investigated is that they appear to transpose by replicative transposition and form pseudo compound transposons with the flanking IS in direct repeat and in which associated genes are simply transferred to the target replicon and lost from the donor.In the accompanying letter Hall raises a number of very serious and wide-ranging criticisms of our recent review article concerning the IS6 family of insertion sequences. She clearly feels that we have undervalued her work and that we question or ignore certain of her in vivo results. This impression is almost certainly the result of the standard of proof we generally apply to mechanistic aspects of transposition where we think it important to identify transposition intermediates including the types of synaptic, strand cleavage and strand transfer complexes involved.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2022-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8722142/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39782322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Designing complex, dynamic yet multi-functional materials and devices is challenging because the design spaces for these materials have numerous interdependent and often conflicting constraints. Taking inspiration from advances in artificial intelligence and their applications in material discovery, we propose a computational method for designing metamorphic DNA-co-polymerized hydrogel structures. The method consists of a coarse-grained simulation and a deep learning-guided optimization system for exploring the immense design space of these structures. Here, we develop a simple numeric simulation of DNA-co-polymerized hydrogel shape change and seek to find designs for structured hydrogels that can fold into the shapes of different Arabic numerals in different actuation states. We train a convolutional neural network to classify and score the geometric outputs of the coarse-grained simulation to provide autonomous feedback for design optimization. We then construct a genetic algorithm that generates and selects large batches of material designs that compete with one another to evolve and converge on optimal objective-matching designs. We show that we are able to explore the large design space and learn important parameters and traits. We identify vital relationships between the material scale size and the range of shape change that can be achieved by individual domains and we elucidate trade-offs between different design parameters. Finally, we discover material designs capable of transforming into multiple different digits in different actuation states.
{"title":"Exploring Material Design Space with a Deep-Learning Guided Genetic Algorithm","authors":"Kuan-Lin Chen, Rebecca Schulman","doi":"10.4230/LIPIcs.DNA.28.4","DOIUrl":"https://doi.org/10.4230/LIPIcs.DNA.28.4","url":null,"abstract":"Designing complex, dynamic yet multi-functional materials and devices is challenging because the design spaces for these materials have numerous interdependent and often conflicting constraints. Taking inspiration from advances in artificial intelligence and their applications in material discovery, we propose a computational method for designing metamorphic DNA-co-polymerized hydrogel structures. The method consists of a coarse-grained simulation and a deep learning-guided optimization system for exploring the immense design space of these structures. Here, we develop a simple numeric simulation of DNA-co-polymerized hydrogel shape change and seek to find designs for structured hydrogels that can fold into the shapes of different Arabic numerals in different actuation states. We train a convolutional neural network to classify and score the geometric outputs of the coarse-grained simulation to provide autonomous feedback for design optimization. We then construct a genetic algorithm that generates and selects large batches of material designs that compete with one another to evolve and converge on optimal objective-matching designs. We show that we are able to explore the large design space and learn important parameters and traits. We identify vital relationships between the material scale size and the range of shape change that can be achieved by individual domains and we elucidate trade-offs between different design parameters. Finally, we discover material designs capable of transforming into multiple different digits in different actuation states.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80896202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bowen Li, N. Mackenzie, Ben Shirt-Ediss, N. Krasnogor, P. Zuliani
A DNA stack nano-device is a bio-computing system that can read and write molecular signals based on DNA-DNA hybridisation and strand displacement. In vitro implementation of the DNA stack faces a number of challenges affecting the performance of the system. In this work, we apply probabilistic model checking to analyse and optimise the DNA stack system. We develop a model framework based on continuous-time Markov chains to quantitatively describe the system behaviour. We use the PRISM probabilistic model checker to answer two important questions: 1) What is the minimum required incubation time to store a signal? And 2) How can we maximise the yield of the system? The results suggest that the incubation time can be reduced from 30 minutes to 5-15 minutes depending on the stack operation stage. In addition, the optimised model shows a 40% increase in the target stack yield. project “Synthetic Portabolomics: Leading the way at the crossroads of the Digital and the Bio Economies” (EP/N031962/1). Krasnogor was supported by the Royal Academy of Engineering under the Chairs in Emerging Technologies scheme.
{"title":"Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking","authors":"Bowen Li, N. Mackenzie, Ben Shirt-Ediss, N. Krasnogor, P. Zuliani","doi":"10.4230/LIPIcs.DNA.28.5","DOIUrl":"https://doi.org/10.4230/LIPIcs.DNA.28.5","url":null,"abstract":"A DNA stack nano-device is a bio-computing system that can read and write molecular signals based on DNA-DNA hybridisation and strand displacement. In vitro implementation of the DNA stack faces a number of challenges affecting the performance of the system. In this work, we apply probabilistic model checking to analyse and optimise the DNA stack system. We develop a model framework based on continuous-time Markov chains to quantitatively describe the system behaviour. We use the PRISM probabilistic model checker to answer two important questions: 1) What is the minimum required incubation time to store a signal? And 2) How can we maximise the yield of the system? The results suggest that the incubation time can be reduced from 30 minutes to 5-15 minutes depending on the stack operation stage. In addition, the optimised model shows a 40% increase in the target stack yield. project “Synthetic Portabolomics: Leading the way at the crossroads of the Digital and the Bio Economies” (EP/N031962/1). Krasnogor was supported by the Royal Academy of Engineering under the Chairs in Emerging Technologies scheme.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87676767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
DNA Strand Displacement (DSD) systems model basic reaction rules, such as toehold-mediated strand displacement and 4-way branch migration, that modify complexes of bound DNA strands. DSD systems have been widely used to design and reason about the correctness of molecular programs, including implementations of logic circuits, neural networks, and Chemical Reaction Networks. Such implementations employ a valuable toolkit of mechanisms – sequences of basic reaction rules – that achieve catalysis, reduce errors (e.g., due to leak), or simulate simple computational units such as logic gates, both in solution and on surfaces. Expanding the DSD toolkit of DSD mechanisms can lead to new and better ways of programming with DNA. Here we introduce a new mechanism, which we call controlled reconfiguration . We describe one example where two single-stranded DSD complexes interact, changing the bonds in both complexes in a way that would not be possible for each independently on its own via the basic reaction rules allowed by the model. We use coupled reconfiguration to refer to instances of controlled reconfiguration in which two reactants change each other in this way. We note that our DSD model disallows pseudoknots and that properties of our coupled reconfiguration construction rely on this restriction of the model. A key feature of our coupled reconfiguration example, which distinguishes it from mechanisms (such as 3-way strand displacement or 4-way branch migration) that are typically used to implement molecular programs, is that the reactants are single-stranded. Leveraging this feature, we show how to use coupled reconfiguration to implement Chemical Reaction Networks (CRNs), with a DSD system that has both single-stranded signals (which represent the species of the CRN) and single-stranded fuels (which drive the CRN reactions). Our implementation also has other desirable properties; for example it is capable of implementing reversible CRNs and uses just two distinct toeholds. We discuss drawbacks of our implementation, particularly the reliance on pseudoknot-freeness for correctness, and suggest directions for future research that can provide further insight on the capabilities and limitations of controlled reconfiguration. computing (DSD) systems. a particularly well-studied abstract model of well-mixed chemical systems, in which many interesting programs can be and have been written [2, 3, 28, 36, 41]. Moreover, arbitrary CRNs can be transformed into DSD systems that implement the original CRN [7, 10, 30, 37, 39].
{"title":"A Coupled Reconfiguration Mechanism for Single-Stranded DNA Strand Displacement Systems","authors":"H. Johnson, A. Condon","doi":"10.4230/LIPIcs.DNA.28.3","DOIUrl":"https://doi.org/10.4230/LIPIcs.DNA.28.3","url":null,"abstract":"DNA Strand Displacement (DSD) systems model basic reaction rules, such as toehold-mediated strand displacement and 4-way branch migration, that modify complexes of bound DNA strands. DSD systems have been widely used to design and reason about the correctness of molecular programs, including implementations of logic circuits, neural networks, and Chemical Reaction Networks. Such implementations employ a valuable toolkit of mechanisms – sequences of basic reaction rules – that achieve catalysis, reduce errors (e.g., due to leak), or simulate simple computational units such as logic gates, both in solution and on surfaces. Expanding the DSD toolkit of DSD mechanisms can lead to new and better ways of programming with DNA. Here we introduce a new mechanism, which we call controlled reconfiguration . We describe one example where two single-stranded DSD complexes interact, changing the bonds in both complexes in a way that would not be possible for each independently on its own via the basic reaction rules allowed by the model. We use coupled reconfiguration to refer to instances of controlled reconfiguration in which two reactants change each other in this way. We note that our DSD model disallows pseudoknots and that properties of our coupled reconfiguration construction rely on this restriction of the model. A key feature of our coupled reconfiguration example, which distinguishes it from mechanisms (such as 3-way strand displacement or 4-way branch migration) that are typically used to implement molecular programs, is that the reactants are single-stranded. Leveraging this feature, we show how to use coupled reconfiguration to implement Chemical Reaction Networks (CRNs), with a DSD system that has both single-stranded signals (which represent the species of the CRN) and single-stranded fuels (which drive the CRN reactions). Our implementation also has other desirable properties; for example it is capable of implementing reversible CRNs and uses just two distinct toeholds. We discuss drawbacks of our implementation, particularly the reliance on pseudoknot-freeness for correctness, and suggest directions for future research that can provide further insight on the capabilities and limitations of controlled reconfiguration. computing (DSD) systems. a particularly well-studied abstract model of well-mixed chemical systems, in which many interesting programs can be and have been written [2, 3, 28, 36, 41]. Moreover, arbitrary CRNs can be transformed into DSD systems that implement the original CRN [7, 10, 30, 37, 39].","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87141530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}