Pub Date : 2023-11-14DOI: 10.1101/2023.11.13.566810
Mattia Chini, Marilena Hnida, Johanna K Kostka, Yu-Nan Chen, Ileana L. Hanganu-Opatz
In the adult brain, structural and functional parameters, such as synaptic sizes and neuronal firing rates, follow right-skewed and heavy-tailed distributions. While this organization is thought of having significant implications, its development is still largely unknown. Here, we address this knowledge gap by investigating a large-scale dataset recorded from the prefrontal cortex (PFC) and the olfactory bulb of mice aged 4-60 postnatal days. We show that firing rates and pairwise correlations have a largely stable distribution shape over age, and that neural activity displays a small-world architecture. Moreover, early brain activity displays an oligarchical organization, i.e., neurons with high firing rates are likely to have hub-like properties. Leveraging neural network modeling, we show that analogously extremely distributed synaptic parameters are necessary to recapitulate the experimental data. Thus, functional and structural parameters in the developing brain are already extremely distributed, suggesting that this organization is preconfigured and not experience-dependent.
{"title":"Extreme distributions in the preconfigured developing brain","authors":"Mattia Chini, Marilena Hnida, Johanna K Kostka, Yu-Nan Chen, Ileana L. Hanganu-Opatz","doi":"10.1101/2023.11.13.566810","DOIUrl":"https://doi.org/10.1101/2023.11.13.566810","url":null,"abstract":"In the adult brain, structural and functional parameters, such as synaptic sizes and neuronal firing rates, follow right-skewed and heavy-tailed distributions. While this organization is thought of having significant implications, its development is still largely unknown. Here, we address this knowledge gap by investigating a large-scale dataset recorded from the prefrontal cortex (PFC) and the olfactory bulb of mice aged 4-60 postnatal days. We show that firing rates and pairwise correlations have a largely stable distribution shape over age, and that neural activity displays a small-world architecture. Moreover, early brain activity displays an oligarchical organization, i.e., neurons with high firing rates are likely to have hub-like properties. Leveraging neural network modeling, we show that analogously extremely distributed synaptic parameters are necessary to recapitulate the experimental data. Thus, functional and structural parameters in the developing brain are already extremely distributed, suggesting that this organization is preconfigured and not experience-dependent.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"38 48","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134953630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1101/2023.11.14.567071
Bruno Rafael Barboza, Janaina Macedo da Silva, Lays Adrianne Mendonca Trajano-Silva, Vinicius de Morais Gomes, Deivid Martins Santos, Antonio Moreira Marques-Neto, Simon Ngao Mule, Juliana Borsoi, Carolina Borsoi Moraes, Martina Muhlenhoff, Walter Colli, Suely K N Marie, Lygia V Pereira, Maria Julia Manso Alves, Giuseppe Palmisano
Glycosylation is one of the most structurally and functionally diverse co- and post-translational modifications in a cell. Addition and removal of glycans, especially to proteins and lipids, characterize this process which have important implications in several biological processes. In mammals, the repeated enzymatic addition of a sialic acid unit to underlying sialic acids (Sia) by polysialyltransferases, including ST8Sia2, leads to the formation of a sugar polymer called polysialic acid (polySia). The functional relevance of polySia has been extensively demonstrated in the nervous system. However, the role of polysialylation in infection is still poorly explored. Previous reports have shown that Trypanosoma cruzi (T. cruzi), a flagellated parasite that causes Chagas disease (CD), changes host sialylation of glycoproteins. To understand the role of host polySia during T. cruzi infection, we used a combination of in silico and experimental tools. We observed that T. cruzi reduces both the expression of the ST8Sia2 and the polysialylation of target substrates. We also found that chemical and genetic inhibition of host ST8Sia2 increased the parasite load in mammalian cells. These findings suggest a novel approach to interfere with parasite infections through modulation of host polysialylation.
{"title":"ST8Sia2 polysialyltransferase protects against infection by Trypanosoma cruzi","authors":"Bruno Rafael Barboza, Janaina Macedo da Silva, Lays Adrianne Mendonca Trajano-Silva, Vinicius de Morais Gomes, Deivid Martins Santos, Antonio Moreira Marques-Neto, Simon Ngao Mule, Juliana Borsoi, Carolina Borsoi Moraes, Martina Muhlenhoff, Walter Colli, Suely K N Marie, Lygia V Pereira, Maria Julia Manso Alves, Giuseppe Palmisano","doi":"10.1101/2023.11.14.567071","DOIUrl":"https://doi.org/10.1101/2023.11.14.567071","url":null,"abstract":"Glycosylation is one of the most structurally and functionally diverse co- and post-translational modifications in a cell. Addition and removal of glycans, especially to proteins and lipids, characterize this process which have important implications in several biological processes. In mammals, the repeated enzymatic addition of a sialic acid unit to underlying sialic acids (Sia) by polysialyltransferases, including ST8Sia2, leads to the formation of a sugar polymer called polysialic acid (polySia). The functional relevance of polySia has been extensively demonstrated in the nervous system. However, the role of polysialylation in infection is still poorly explored. Previous reports have shown that Trypanosoma cruzi (T. cruzi), a flagellated parasite that causes Chagas disease (CD), changes host sialylation of glycoproteins. To understand the role of host polySia during T. cruzi infection, we used a combination of in silico and experimental tools. We observed that T. cruzi reduces both the expression of the ST8Sia2 and the polysialylation of target substrates. We also found that chemical and genetic inhibition of host ST8Sia2 increased the parasite load in mammalian cells. These findings suggest a novel approach to interfere with parasite infections through modulation of host polysialylation.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"48 20","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1101/2023.11.14.567099
Einat Segev, Yemima Duchin Rapp, Lilach Yuda, Dor Matsliyah, Ilya V. Kublanov
Horizontal gene transfer (HGT) is a pivotal mechanism driving bacterial evolution, conferring adaptability within dynamic marine ecosystems. Among HGT mechanisms, conjugation mediated by Type IV secretion systems (T4SSs) plays a central role in the ecological success of marine bacteria. However, the triggers initiating conjugation events in the marine environment are not well understood. Roseobacters, abundant marine bacteria commonly associated with algae, possess a multitude of plasmids encoding T4SSs. Many Roseobacters are heterotrophic bacteria that rely on algal secreted compounds for supporting bacterial growth. Algal compounds therefore attract bacteria and promote colonization, including attachment to algal cells. Bacterial proximity, cell-to-cell contact, and attachment, can all foster HGT. Hence, we hypothesized that algal exudates, acting as chemoattractants for bacteria, may function as cues promoting bacterial HGT. Examination of various Roseobacters demonstrated that the genomic location of the T4SS impacts its functionality; a bacterial strain harboring a chromosomal-encoded T4SS does not perform conjugation, while a strain of the same species carrying a plasmid-encoded T4SS exhibits functional conjugation capability. Subsequently, we probed the influence of algal exudates on bacterial conjugation dynamics. Our findings revealed that algal exudates enhance plasmid transfer through conjugation but do not modulate the transcription of the conjugative machinery genes. These observations suggest that the bacterial responses to algal hosts evolved to correlate with an increased likelihood of encountering compatible partners for successful conjugation. Furthermore, since specific algae attract distinct bacterial populations, algae influence potential partners for genetic exchange and may shape the trajectory of bacterial evolution in the marine environment.
{"title":"Algal Exudates Promote Conjugation in Marine Roseobacters","authors":"Einat Segev, Yemima Duchin Rapp, Lilach Yuda, Dor Matsliyah, Ilya V. Kublanov","doi":"10.1101/2023.11.14.567099","DOIUrl":"https://doi.org/10.1101/2023.11.14.567099","url":null,"abstract":"Horizontal gene transfer (HGT) is a pivotal mechanism driving bacterial evolution, conferring adaptability within dynamic marine ecosystems. Among HGT mechanisms, conjugation mediated by Type IV secretion systems (T4SSs) plays a central role in the ecological success of marine bacteria. However, the triggers initiating conjugation events in the marine environment are not well understood. Roseobacters, abundant marine bacteria commonly associated with algae, possess a multitude of plasmids encoding T4SSs. Many Roseobacters are heterotrophic bacteria that rely on algal secreted compounds for supporting bacterial growth. Algal compounds therefore attract bacteria and promote colonization, including attachment to algal cells. Bacterial proximity, cell-to-cell contact, and attachment, can all foster HGT. Hence, we hypothesized that algal exudates, acting as chemoattractants for bacteria, may function as cues promoting bacterial HGT. Examination of various Roseobacters demonstrated that the genomic location of the T4SS impacts its functionality; a bacterial strain harboring a chromosomal-encoded T4SS does not perform conjugation, while a strain of the same species carrying a plasmid-encoded T4SS exhibits functional conjugation capability. Subsequently, we probed the influence of algal exudates on bacterial conjugation dynamics. Our findings revealed that algal exudates enhance plasmid transfer through conjugation but do not modulate the transcription of the conjugative machinery genes. These observations suggest that the bacterial responses to algal hosts evolved to correlate with an increased likelihood of encountering compatible partners for successful conjugation. Furthermore, since specific algae attract distinct bacterial populations, algae influence potential partners for genetic exchange and may shape the trajectory of bacterial evolution in the marine environment.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"48 19","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1101/2023.11.14.566933
Corey Thomas, Lisbeth Avalos-Irving, Jorge Victorino, Sydney Green, Morgan Andrews, Naisha Rodrigues, Sarah Ebirim, Ayden Mudd, Jamie B Towle-Weicksel
DNA Polymerase θ (Pol θ or POLQ) is primarily involved in repairing double-stranded breaks in DNA through the alternative pathway known as microhomology-mediated end joining (MMEJ) or theta-mediated end joining (TMEJ). Unlike other DNA repair polymerases, Pol θ is thought to be highly error prone, yet critical for cell survival. We have identified several mutations in the POLQ gene from human melanoma tumors. Through biochemical analysis, we have demonstrated that all three cancer-associated variants experienced altered DNA polymerase activity including a propensity for incorrect nucleotide selection and reduced polymerization rates compared to WT Pol θ. Moreover, the variants are 30 fold less efficient at incorporating a nucleotide during repair and up to 70 fold less accurate at selecting the correct nucleotide opposite a templating base. Taken together, this suggests that aberrant Pol θ has reduced DNA repair capabilities and may also contribute to increased mutagenesis. While this may be beneficial to normal cell survival, the variants were identified in established tumors suggesting that cancer cells may use this promiscuous polymerase to its advantage to promote metastasis and drug resistance.
DNA聚合酶θ (Pol θ或POLQ)主要通过微同源介导的末端连接(MMEJ)或theta介导的末端连接(TMEJ)途径参与DNA双链断裂的修复。与其他DNA修复聚合酶不同，Pol θ被认为是高度容易出错的，但对细胞存活至关重要。我们已经从人类黑色素瘤肿瘤中发现了POLQ基因的几个突变。通过生化分析，我们已经证明，与WT Pol θ相比，所有三种癌症相关变异都经历了DNA聚合酶活性的改变，包括不正确核苷酸选择的倾向和聚合速率的降低。此外，这些变体在修复过程中结合核苷酸的效率降低了30倍，在选择与模板碱基相反的正确核苷酸时的准确性降低了70倍。综上所述，这表明异常的Pol θ降低了DNA修复能力，也可能导致突变增加。虽然这可能有利于正常细胞的存活，但在已建立的肿瘤中发现了这些变异，这表明癌细胞可能利用这种混杂聚合酶来促进转移和耐药性。
{"title":"Melanoma-derived DNA polymerase theta variants exhibit altered DNA polymerase activity","authors":"Corey Thomas, Lisbeth Avalos-Irving, Jorge Victorino, Sydney Green, Morgan Andrews, Naisha Rodrigues, Sarah Ebirim, Ayden Mudd, Jamie B Towle-Weicksel","doi":"10.1101/2023.11.14.566933","DOIUrl":"https://doi.org/10.1101/2023.11.14.566933","url":null,"abstract":"DNA Polymerase θ (Pol θ or POLQ) is primarily involved in repairing double-stranded breaks in DNA through the alternative pathway known as microhomology-mediated end joining (MMEJ) or theta-mediated end joining (TMEJ). Unlike other DNA repair polymerases, Pol θ is thought to be highly error prone, yet critical for cell survival. We have identified several mutations in the POLQ gene from human melanoma tumors. Through biochemical analysis, we have demonstrated that all three cancer-associated variants experienced altered DNA polymerase activity including a propensity for incorrect nucleotide selection and reduced polymerization rates compared to WT Pol θ. Moreover, the variants are 30 fold less efficient at incorporating a nucleotide during repair and up to 70 fold less accurate at selecting the correct nucleotide opposite a templating base. Taken together, this suggests that aberrant Pol θ has reduced DNA repair capabilities and may also contribute to increased mutagenesis. While this may be beneficial to normal cell survival, the variants were identified in established tumors suggesting that cancer cells may use this promiscuous polymerase to its advantage to promote metastasis and drug resistance.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"51 10","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1101/2023.11.14.567005
Beth A James, Hishikha Reesaul, Sidra Kashif, Mahoobeh Behruznia, Conor J Meehan, Maria Rosa Domingo Sananes, Alasdair T M Hubbard
Trimethoprim is recommended as a first-line treatment of urinary tract infections (UTIs) in the UK. In 2018, 31.4% of Escherichia coli isolated from UTIs in England were trimethoprim resistant, leading to overreliance on other first and second-line antibiotics. Here, we assessed whether prior selection with trimethoprim results in collateral effects to other antibiotics recommended for the treatment of UTIs. As collateral effects, we considered changes in susceptibility, mutation-selection window and population establishment probability. We selected 10 trimethoprim-resistant derivatives from three clinical isolates of uropathogenic Escherichia coli. We found that mutations conferring trimethoprim resistance did not have any collateral effects to fosfomycin. In contrast, resistance to trimethoprim resulted in decreased susceptibility (collateral resistance) to nitrofurantoin, below the clinical breakpoint, and narrowed the mutation-selection window thereby reducing the maximum concentration for selection of nitrofurantoin resistance mutations. Our analyses demonstrate that multiple collateral responses should be accounted for when predicting and optimising antibiotic use, limiting future AMR emergence.
{"title":"The effect of antibiotic selection on collateral effects and evolvability of uropathogenic Escherichia coli","authors":"Beth A James, Hishikha Reesaul, Sidra Kashif, Mahoobeh Behruznia, Conor J Meehan, Maria Rosa Domingo Sananes, Alasdair T M Hubbard","doi":"10.1101/2023.11.14.567005","DOIUrl":"https://doi.org/10.1101/2023.11.14.567005","url":null,"abstract":"Trimethoprim is recommended as a first-line treatment of urinary tract infections (UTIs) in the UK. In 2018, 31.4% of Escherichia coli isolated from UTIs in England were trimethoprim resistant, leading to overreliance on other first and second-line antibiotics. Here, we assessed whether prior selection with trimethoprim results in collateral effects to other antibiotics recommended for the treatment of UTIs. As collateral effects, we considered changes in susceptibility, mutation-selection window and population establishment probability. We selected 10 trimethoprim-resistant derivatives from three clinical isolates of uropathogenic Escherichia coli. We found that mutations conferring trimethoprim resistance did not have any collateral effects to fosfomycin. In contrast, resistance to trimethoprim resulted in decreased susceptibility (collateral resistance) to nitrofurantoin, below the clinical breakpoint, and narrowed the mutation-selection window thereby reducing the maximum concentration for selection of nitrofurantoin resistance mutations. Our analyses demonstrate that multiple collateral responses should be accounted for when predicting and optimising antibiotic use, limiting future AMR emergence.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"45 23","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1101/2023.11.13.566834
Roberta Aralla, Claire Pauley, Christine Koeppl
The sound localisation behaviour of the nocturnally hunting barn owl and its underlying neural computations is a textbook example of neuroethology. Differences in sound timing and level at the two ears are integrated in a series of well characterised steps, from brainstem to inferior colliculus, resulting in a topographical neural representation of auditory space. It remains an important question of brain evolution how this specialised case derived from a more plesiomorphic pattern. The present study is the first to match physiology and anatomical subregions in the non-owl avian inferior colliculus. Single-unit responses in the chicken inferior colliculus were tested for selectivity to different frequencies and to the binaural difference cues. Their anatomical origin was reconstructed with the help of electrolytic lesions and immunohistochemical identification of different subregions of the inferior colliculus, based on previous characterisations in owl and chicken. In contrast to barn owl, there was no distinct differentiation of responses in the different subregions. We found neural topographies for both binaural cues but no evidence for a coherent representation of auditory space. The results are consistent with previous work in pigeon inferior colliculus and chicken higher-order midbrain and suggest a plesiomorphic condition of multisensory integration in the midbrain that is dominated by lateral panoramic vision.
{"title":"Differences in the neural representation of binaural sound localization cues in the auditory midbrain of chicken and barn owl","authors":"Roberta Aralla, Claire Pauley, Christine Koeppl","doi":"10.1101/2023.11.13.566834","DOIUrl":"https://doi.org/10.1101/2023.11.13.566834","url":null,"abstract":"The sound localisation behaviour of the nocturnally hunting barn owl and its underlying neural computations is a textbook example of neuroethology. Differences in sound timing and level at the two ears are integrated in a series of well characterised steps, from brainstem to inferior colliculus, resulting in a topographical neural representation of auditory space. It remains an important question of brain evolution how this specialised case derived from a more plesiomorphic pattern. The present study is the first to match physiology and anatomical subregions in the non-owl avian inferior colliculus. Single-unit responses in the chicken inferior colliculus were tested for selectivity to different frequencies and to the binaural difference cues. Their anatomical origin was reconstructed with the help of electrolytic lesions and immunohistochemical identification of different subregions of the inferior colliculus, based on previous characterisations in owl and chicken. In contrast to barn owl, there was no distinct differentiation of responses in the different subregions. We found neural topographies for both binaural cues but no evidence for a coherent representation of auditory space. The results are consistent with previous work in pigeon inferior colliculus and chicken higher-order midbrain and suggest a plesiomorphic condition of multisensory integration in the midbrain that is dominated by lateral panoramic vision.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1101/2023.11.14.567009
Emmanuelle Wilhelm, Mikael Poirier, Mikael Bedard, Patrick P. McDonald, Pierre Lavigne, Christie Hunter, Brendan Bell
The human immunodeficiency virus (HIV) integrates into the host genome forming latent cellular reservoirs that are an obstacle for cure or remission strategies. Viral transcription is the first step in the control of latency and depends upon the hijacking of the host cell RNA polymerase II (Pol II) machinery by the 5' HIV LTR. Consequently, block and lock or shock and kill strategies for an HIV cure depend upon a full understanding of HIV transcriptional control. The HIV trans-activating protein, Tat, controls HIV latency as part of a positive feed-forward loop that strongly activates HIV transcription. The recognition of the TATA box and adjacent sequences of HIV essential for Tat trans-activation (TASHET) of the core promoter by host cell pre initiation complexes of HIV (PICH) has been shown to be necessary for Tat trans-activation, yet the protein composition of PICH has remained obscure. Here DNA-affinity chromatography was employed to identify the mitotic deacetylase complex (MiDAC) as selectively recognizing TASHET. Using biophysical techniques, we show that the MiDAC subunit DNTTIP1 binds directly to TASHET, in part via its CTGC DNA motifs. Using co-immunoprecipitation assays, we show that DNTTIP1 interacts with MiDAC subunits MIDEAS and HDAC1/2. The Tat-interacting protein, NAT10, is also present in HIV-bound MiDAC. Gene silencing revealed a functional role for DNTTIP1, MIDEAS, and NAT10 in HIV expression in cellulo. Furthermore, point mutations in TASHET that prevent DNTTIP1 binding block the reactivation of HIV by latency reversing agents (LRA) that act via the P-TEFb/7SK axis in a model of latency. Our data reveal a key role for MiDAC subunits DNTTIP1, MIDEAS, as well as NAT10, in Tat-activated HIV transcription and latency. DNTTIP1, MIDEAS and NAT10 emerge as cell cycle-regulated host cell transcription factors that can control HIV latency, and as new drug targets for HIV cure strategies.
人类免疫缺陷病毒(HIV)整合到宿主基因组中形成潜在的细胞储存库，这是治疗或缓解策略的障碍。病毒转录是控制潜伏期的第一步，依赖于宿主细胞RNA聚合酶II (Pol II)机制被5' HIV LTR劫持。因此，阻断和锁定或休克和杀死HIV治疗策略取决于对HIV转录控制的充分理解。HIV反式激活蛋白Tat作为一个正前馈循环的一部分控制HIV潜伏期，该循环强烈激活HIV转录。宿主细胞HIV预起始复合物(PICH)对核心启动子Tat反式激活(taset)所必需的TATA盒和邻近的HIV序列的识别已被证明是Tat反式激活所必需的，但PICH的蛋白质组成仍然不清楚。本文采用dna亲和层析法鉴定有丝分裂脱乙酰酶复合体(MiDAC)选择性识别TASHET。利用生物物理技术，我们发现MiDAC亚基DNTTIP1直接与TASHET结合，部分通过其CTGC DNA基序。通过共免疫沉淀实验，我们发现DNTTIP1与MiDAC亚基MIDEAS和HDAC1/2相互作用。tat相互作用蛋白NAT10也存在于hiv结合的MiDAC中。基因沉默揭示了DNTTIP1、MIDEAS和NAT10在细胞中HIV表达中的功能作用。此外，TASHET中阻止DNTTIP1结合的点突变阻断了潜伏期逆转剂(LRA)在潜伏期模型中通过P-TEFb/7SK轴起作用的HIV的再激活。我们的数据揭示了MiDAC亚基DNTTIP1、MIDEAS和NAT10在tat激活的HIV转录和潜伏期中发挥关键作用。DNTTIP1、MIDEAS和NAT10是细胞周期调控的宿主细胞转录因子，可控制HIV潜伏期，是HIV治愈策略的新药物靶点。
{"title":"Mitotic deacetylase complex (MiDAC) recognizes the HIV-1 core promoter to control Tat-activated transcription and latency","authors":"Emmanuelle Wilhelm, Mikael Poirier, Mikael Bedard, Patrick P. McDonald, Pierre Lavigne, Christie Hunter, Brendan Bell","doi":"10.1101/2023.11.14.567009","DOIUrl":"https://doi.org/10.1101/2023.11.14.567009","url":null,"abstract":"The human immunodeficiency virus (HIV) integrates into the host genome forming latent cellular reservoirs that are an obstacle for cure or remission strategies. Viral transcription is the first step in the control of latency and depends upon the hijacking of the host cell RNA polymerase II (Pol II) machinery by the 5' HIV LTR. Consequently, block and lock or shock and kill strategies for an HIV cure depend upon a full understanding of HIV transcriptional control. The HIV trans-activating protein, Tat, controls HIV latency as part of a positive feed-forward loop that strongly activates HIV transcription. The recognition of the TATA box and adjacent sequences of HIV essential for Tat trans-activation (TASHET) of the core promoter by host cell pre initiation complexes of HIV (PICH) has been shown to be necessary for Tat trans-activation, yet the protein composition of PICH has remained obscure. Here DNA-affinity chromatography was employed to identify the mitotic deacetylase complex (MiDAC) as selectively recognizing TASHET. Using biophysical techniques, we show that the MiDAC subunit DNTTIP1 binds directly to TASHET, in part via its CTGC DNA motifs. Using co-immunoprecipitation assays, we show that DNTTIP1 interacts with MiDAC subunits MIDEAS and HDAC1/2. The Tat-interacting protein, NAT10, is also present in HIV-bound MiDAC. Gene silencing revealed a functional role for DNTTIP1, MIDEAS, and NAT10 in HIV expression in cellulo. Furthermore, point mutations in TASHET that prevent DNTTIP1 binding block the reactivation of HIV by latency reversing agents (LRA) that act via the P-TEFb/7SK axis in a model of latency. Our data reveal a key role for MiDAC subunits DNTTIP1, MIDEAS, as well as NAT10, in Tat-activated HIV transcription and latency. DNTTIP1, MIDEAS and NAT10 emerge as cell cycle-regulated host cell transcription factors that can control HIV latency, and as new drug targets for HIV cure strategies.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"47 23","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134992202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1101/2023.11.14.567022
Elena Georgiou, Javier Cabello Garcia, Yongzheng Xing, Stefan Howorka
Rigid DNA nanostructures that bind to floppy bilayer membranes are of fundamental interest as they replicate biological cytoskeletons for synthetic biology, biosensing, and biological research. Here, we establish principles underpinning the controlled interaction of DNA structures and lipid bilayers. As membrane anchors mediate interaction, more than 20 versions of a core DNA nanostructure are built each carrying up to five individual cholesterol anchors of different steric accessibility within the 3D geometry. The structures binding to membrane vesicles of tunable curvature is determined with ensemble methods and by single-molecule localization microscopy. This screen yields quantitative and unexpected insight on which steric anchor points cause efficient binding. Strikingly, defined nanostructures with a single molecular anchor discriminate effectively between vesicles of different nanoscale curvatures which may be exploited to discern diagnostically relevant membrane vesicles based on size. Furthermore, we reveal anchor-mediated bilayer interaction to be co-controlled by non-lipidated DNA regions and localized membrane curvatures stemming from heterogenous lipid composition, which modifies existing biophysical models. Our study extends DNA nanotechnology to control interactions with bilayer membranes and thereby facilitate the design of nanodevices for vesicle-based diagnostics, biosensing, and protocells.
{"title":"DNA Origami Lipid Membrane Interactions Defined at Single-Molecular Resolution","authors":"Elena Georgiou, Javier Cabello Garcia, Yongzheng Xing, Stefan Howorka","doi":"10.1101/2023.11.14.567022","DOIUrl":"https://doi.org/10.1101/2023.11.14.567022","url":null,"abstract":"Rigid DNA nanostructures that bind to floppy bilayer membranes are of fundamental interest as they replicate biological cytoskeletons for synthetic biology, biosensing, and biological research. Here, we establish principles underpinning the controlled interaction of DNA structures and lipid bilayers. As membrane anchors mediate interaction, more than 20 versions of a core DNA nanostructure are built each carrying up to five individual cholesterol anchors of different steric accessibility within the 3D geometry. The structures binding to membrane vesicles of tunable curvature is determined with ensemble methods and by single-molecule localization microscopy. This screen yields quantitative and unexpected insight on which steric anchor points cause efficient binding. Strikingly, defined nanostructures with a single molecular anchor discriminate effectively between vesicles of different nanoscale curvatures which may be exploited to discern diagnostically relevant membrane vesicles based on size. Furthermore, we reveal anchor-mediated bilayer interaction to be co-controlled by non-lipidated DNA regions and localized membrane curvatures stemming from heterogenous lipid composition, which modifies existing biophysical models. Our study extends DNA nanotechnology to control interactions with bilayer membranes and thereby facilitate the design of nanodevices for vesicle-based diagnostics, biosensing, and protocells.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"39 18","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134992484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The mutants insensitive to ethylene are helpful in deciphering the role of ethylene in plant development. We isolated an ethylene-insensitive tomato (Solanum lycopersicum) mutant by screening for acetylene-resistant (atr-1) seedlings. The atr-1 mutant displayed resistance to kinetin, suggesting attenuation of the ethylene sensing response. atr-1 also exhibited resistance to ABA- and glucose-mediated inhibition of seed germination. Unlike the Never-ripe (Nr) mutant, atr-1 seedlings were resistant to glucose, indicating ethylene sensing in atr-1 is located in a component distinct from Nr. Metabolically, atr-1 seedlings had lower levels of amino acids but higher levels of several phytohormones, including ABA. atr-1 plants grew faster and produced more flowers, leading to a higher fruit set. However, the atr-1 fruits took a longer duration to reach the red-ripe (RR) stage. The ripened atr-1 fruits had higher β-carotene levels, retained high β-carotene and lycopene levels post-RR stage. The metabolome profiles of post-RR stage atr-1 fruits revealed increased levels of sugars. The atr-1 had a P279L mutation in the GAF domain of the ETR4, a key ethylene receptor regulating tomato ripening. Our study highlights that novel alleles in ethylene receptors may aid in enhancing the nutritional quality of tomato.
{"title":"A tomato ethylene-insensitive mutant displays altered growth and higher β-carotene levels in fruit","authors":"Suresh Kumar Gupta, Parankusam Santisree, Prateek Gupta, Himabindu Vasuki Kilambi, Yellamaraju Sreelakshmi, Rameshwar Sharma","doi":"10.1101/2023.11.14.566984","DOIUrl":"https://doi.org/10.1101/2023.11.14.566984","url":null,"abstract":"The mutants insensitive to ethylene are helpful in deciphering the role of ethylene in plant development. We isolated an ethylene-insensitive tomato (Solanum lycopersicum) mutant by screening for acetylene-resistant (atr-1) seedlings. The atr-1 mutant displayed resistance to kinetin, suggesting attenuation of the ethylene sensing response. atr-1 also exhibited resistance to ABA- and glucose-mediated inhibition of seed germination. Unlike the Never-ripe (Nr) mutant, atr-1 seedlings were resistant to glucose, indicating ethylene sensing in atr-1 is located in a component distinct from Nr. Metabolically, atr-1 seedlings had lower levels of amino acids but higher levels of several phytohormones, including ABA. atr-1 plants grew faster and produced more flowers, leading to a higher fruit set. However, the atr-1 fruits took a longer duration to reach the red-ripe (RR) stage. The ripened atr-1 fruits had higher β-carotene levels, retained high β-carotene and lycopene levels post-RR stage. The metabolome profiles of post-RR stage atr-1 fruits revealed increased levels of sugars. The atr-1 had a P279L mutation in the GAF domain of the ETR4, a key ethylene receptor regulating tomato ripening. Our study highlights that novel alleles in ethylene receptors may aid in enhancing the nutritional quality of tomato.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"41 7","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134992555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1101/2023.11.10.566598
Tung D Nguyen, Mihir K Rao, Shaiva P Dhyani, Justin M Banks, Michael A Winek, Julka Michalkiewicz, Monica Y Lee
Endothelial cells (ECs) form the innermost lining of the vasculature and serve a pivotal role in preventing age-related vascular disease. Endothelial health relies on the proper nucleocytoplasmic shuttling of transcription factors via nuclear pore complexes (NPCs). Emerging studies report NPC degradation with natural aging, suggesting impaired nucleocytoplasmic transport in age-related EC dysfunction. We herein identify nucleoporin93 (Nup93), a crucial structural NPC protein, as an indispensable player for vascular protection. Endothelial Nup93 protein levels are significantly reduced in the vasculature of aged mice, paralleling observations of Nup93 loss when using in vitro models of endothelial aging. Mechanistically, we find that loss of Nup93 impairs NPC transport, leading to the nuclear accumulation of Yap and downstream inflammation. Collectively, our findings indicate maintenance of endothelial Nup93 as a key determinant of EC health, where aging targets endothelial Nup93 levels to impair NPC function as a novel mechanism for EC senescence and vascular aging.
{"title":"Nucleoporin93 (Nup93) Limits Yap Activity to Prevent Endothelial Cell Senescence","authors":"Tung D Nguyen, Mihir K Rao, Shaiva P Dhyani, Justin M Banks, Michael A Winek, Julka Michalkiewicz, Monica Y Lee","doi":"10.1101/2023.11.10.566598","DOIUrl":"https://doi.org/10.1101/2023.11.10.566598","url":null,"abstract":"Endothelial cells (ECs) form the innermost lining of the vasculature and serve a pivotal role in preventing age-related vascular disease. Endothelial health relies on the proper nucleocytoplasmic shuttling of transcription factors via nuclear pore complexes (NPCs). Emerging studies report NPC degradation with natural aging, suggesting impaired nucleocytoplasmic transport in age-related EC dysfunction. We herein identify nucleoporin93 (Nup93), a crucial structural NPC protein, as an indispensable player for vascular protection. Endothelial Nup93 protein levels are significantly reduced in the vasculature of aged mice, paralleling observations of Nup93 loss when using in vitro models of endothelial aging. Mechanistically, we find that loss of Nup93 impairs NPC transport, leading to the nuclear accumulation of Yap and downstream inflammation. Collectively, our findings indicate maintenance of endothelial Nup93 as a key determinant of EC health, where aging targets endothelial Nup93 levels to impair NPC function as a novel mechanism for EC senescence and vascular aging.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"36 6","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134992828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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