Genomics, Proteomics & Bioinformatics最新文献_第3页

Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes 基于序列的功能元基因组学揭示了环境微生物组中功能 CopA 的新的自然多样性。

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-12-01 DOI: 10.1016/j.gpb.2022.08.006

Wenjun Li , Likun Wang , Xiaofang Li , Xin Zheng , Michael F. Cohen , Yong-Xin Liu

Exploring the natural diversity of functional genes/proteins from environmental DNA in high throughput remains challenging. In this study, we developed a sequence-based functional metagenomics procedure for mining the diversity of copper (Cu) resistance gene copA in global microbiomes, by combining the metagenomic assembly technology, local BLAST, evolutionary trace analysis (ETA), chemical synthesis, and conventional functional genomics. In total, 87 metagenomes were collected from a public database and subjected to copA detection, resulting in 93,899 hits. Manual curation of 1214 hits of high confidence led to the retrieval of 517 unique CopA candidates, which were further subjected to ETA. Eventually, 175 novel copA sequences of high quality were discovered. Phylogenetic analysis showed that almost all these putative CopA proteins were distantly related to known CopA proteins, with 55 sequences from totally unknown species. Ten novel and three known copA genes were chemically synthesized for further functional genomic tests using the Cu-sensitive Escherichia coli (ΔcopA). The growth test and Cu uptake determination showed that five novel clones had positive effects on host Cu resistance and uptake. One recombinant harboring copA-like 15 (copAL15) successfully restored Cu resistance of the host with a substantially enhanced Cu uptake. Two novel copA genes were fused with the gfp gene and expressed in E. coli for microscopic observation. Imaging results showed that they were successfully expressed and their proteins were localized to the membrane. The results here greatly expand the diversity of known CopA proteins, and the sequence-based procedure developed overcomes biases in length, screening methods, and abundance of conventional functional metagenomics.

从环境 DNA 中高通量探索功能基因/蛋白质的自然多样性仍然是一项挑战。在这项研究中，我们开发了一种基于序列的功能元基因组学程序，通过结合元基因组组装技术、局部 BLAST、进化痕量分析（ETA）、化学合成和传统功能基因组学，挖掘全球微生物组中铜（Cu）抗性基因 copA 的多样性。研究人员从公共数据库中收集了 87 个元基因组，并对其进行了 copA 检测，结果发现了 93,899 条命中信息。在对 1214 个高置信度的点击进行人工整理后，检索到 517 个独特的 CopA 候选者，并对其进行了进一步的 ETA 分析。最终，发现了 175 个高质量的新型 CopA 序列。系统进化分析表明，几乎所有这些假定的 CopA 蛋白都与已知的 CopA 蛋白关系密切，其中 55 个序列来自完全未知的物种。我们用化学方法合成了 10 个新的和 3 个已知的 CopA 基因，并利用对铜敏感的大肠杆菌（ΔcopA）进行了进一步的功能基因组测试。生长试验和铜吸收测定结果表明，五个新克隆对宿主的铜抗性和铜吸收有积极影响。其中一个携带 copA-like 15（copAL15）的重组体成功地恢复了宿主对铜的抗性，并大大提高了铜的吸收率。两个新型 copA 基因与 gfp 基因融合，并在大肠杆菌中表达，以进行显微观察。成像结果表明，这两个基因成功表达，其蛋白定位于膜。这些结果大大扩展了已知 CopA 蛋白的多样性，而且所开发的基于序列的程序克服了传统功能元组学在长度、筛选方法和丰度方面的偏差。

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引用次数: 0

High Sensitivity of Shotgun Metagenomic Sequencing in Colon Tissue Biopsy by Host DNA Depletion Shotgun宏基因组测序在宿主DNA缺失结肠组织活检中的高灵敏度。

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-12-01 DOI: 10.1016/j.gpb.2022.09.003

Wing Yin Cheng , Wei-Xin Liu , Yanqiang Ding , Guoping Wang , Yu Shi , Eagle S.H. Chu , Sunny Wong , Joseph J.Y. Sung , Jun Yu

The high host genetic background of tissue biopsies hinders the application of shotgun metagenomic sequencing in characterizing the tissue microbiota. We proposed an optimized method that removed host DNA from colon biopsies and examined the effect on metagenomic analysis. Human or mouse colon biopsies were divided into two groups, with one group undergoing host DNA depletion and the other serving as the control. Host DNA was removed through differential lysis of mammalian and bacterial cells before sequencing. The impact of host DNA depletion on microbiota was compared based on phylogenetic diversity analyses and regression analyses. Removing host DNA enhanced bacterial sequencing depth and improved species discovery, increasing bacterial reads by 2.46 ± 0.20 folds while reducing host reads by 6.80% ± 1.06%. Moreover, 2.40 times more of bacterial species were detected after host DNA depletion. This was confirmed from mouse colon tissues, increasing bacterial reads by 5.46 ± 0.42 folds while decreasing host reads by 10.2% ± 0.83%. Similarly, significantly more bacterial species were detected in the mouse colon tissue upon host DNA depletion (P < 0.001). Furthermore, an increased microbial richness was evident in the host DNA-depleted samples compared with non-depleted controls in human colon biopsies and mouse colon tissues (P < 0.001). Our optimized method of host DNA depletion improves the sensitivity of shotgun metagenomic sequencing in bacteria detection in the biopsy, which may yield a more accurate taxonomic profile of the tissue microbiota and identify bacteria that are important for disease initiation or progression.

组织活检的高宿主遗传背景阻碍了霰弹枪宏基因组测序在组织微生物群特征中的应用。我们提出了一种从结肠活检中去除宿主DNA的优化方法，并研究了对宏基因组分析的影响。人类或小鼠结肠活检分为两组，一组进行宿主DNA消耗，另一组作为对照。宿主dna在测序前通过哺乳动物和细菌细胞的差异裂解去除。通过系统发育多样性分析和回归分析，比较了宿主DNA缺失对微生物群的影响。去除宿主DNA可提高细菌测序深度并改善物种发现，细菌reads增加2.46±0.20倍，而宿主reads减少6.80%±1.06%。此外，宿主DNA缺失后检测到的细菌种类增加了3.40倍。小鼠结肠组织证实了这一点，细菌的reads增加了5.46±0.42倍，而宿主的reads减少了10.2%±0.83%。同样，在宿主DNA缺失后，小鼠结肠组织中检测到的物种明显更多(P

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引用次数: 0

T2T-YAO Reference Genome of Han Chinese — New Step in Advancing Precision Medicine in China 汉族T2T-YAO参考基因组-中国精准医学发展的新步伐。

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-12-01 DOI: 10.1016/j.gpb.2023.09.001

Xue Zhang

引用次数: 0

The Proteome Landscape of Human Placentas for Monochorionic Twins with Selective Intrauterine Growth Restriction 选择性宫内生长受限的单绒毛膜双胎人类胎盘的蛋白质组图谱

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-12-01 DOI: 10.1016/j.gpb.2023.03.002

Xin-Lu Meng , Peng-Bo Yuan , Xue-Ju Wang , Jing Hang , Xiao-Ming Shi , Yang-Yu Zhao , Yuan Wei

In perinatal medicine, intrauterine growth restriction (IUGR) is one of the greatest challenges. The etiology of IUGR is multifactorial, but most cases are thought to arise from placental insufficiency. However, identifying the placental cause of IUGR can be difficult due to numerous confounding factors. Selective IUGR (sIUGR) would be a good model to investigate how impaired placentation affects fetal development, as the growth discordance between monochorionic twins cannot be explained by confounding genetic or maternal factors. Herein, we constructed and analyzed the placental proteomic profiles of IUGR twins and normal cotwins. Specifically, we identified a total of 5481 proteins, of which 233 were differentially expressed (57 up-regulated and 176 down-regulated) in IUGR twins. Bioinformatics analysis indicates that these differentially expressed proteins (DEPs) are mainly associated with cardiovascular system development and function, organismal survival, and organismal development. Notably, 34 DEPs are significantly enriched in angiogenesis, and diminished placental angiogenesis in IUGR twins has been further elaborately confirmed. Moreover, we found decreased expression of metadherin (MTDH) in the placentas of IUGR twins and demonstrated that MTDH contributes to placental angiogenesis and fetal growth in vitro. Collectively, our findings reveal the comprehensive proteomic signatures of placentas for sIUGR twins, and the DEPs identified may provide in-depth insights into the pathogenesis of placental dysfunction and subsequent impaired fetal growth.

在围产医学中，宫内生长受限（IUGR）是最大的挑战之一。IUGR 的病因是多方面的，但大多数病例被认为是由胎盘功能不全引起的。然而，由于混杂因素较多，确定 IUGR 的胎盘病因可能比较困难。选择性 IUGR（sIUGR）是研究胎盘功能受损如何影响胎儿发育的一个很好的模型，因为单绒毛膜双胎之间的生长不一致无法用遗传或母体因素来解释。在此，我们构建并分析了IUGR双胞胎和正常同胎双胞胎的胎盘蛋白质组图谱。具体来说，我们共鉴定出5481个蛋白质，其中233个蛋白质在IUGR双胞胎中存在差异表达（57个上调，176个下调）。生物信息学分析表明，这些差异表达蛋白（DEPs）主要与心血管系统发育和功能、机体存活和机体发育有关。值得注意的是，34 个 DEPs 在血管生成中明显富集，而 IUGR 双胞胎胎盘血管生成的减少也得到了进一步的详细证实。此外，我们还发现IUGR双胞胎胎盘中的偏粘连蛋白（MTDH）表达减少，并证明MTDH有助于胎盘血管生成和胎儿体外生长。总之，我们的研究结果揭示了sIUGR双胞胎胎盘的综合蛋白质组特征，所发现的DEPs可能会为胎盘功能障碍及随后的胎儿生长受损的发病机制提供深入的见解。

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引用次数: 0

Comprehensive Characterization and Global Transcriptome Analysis of Human Fetal Liver Terminal Erythropoiesis 人类胎儿肝脏末期红细胞生成的全面特征描述和全局转录组分析

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-12-01 DOI: 10.1016/j.gpb.2023.07.001

Yongshuai Han , Shihui Wang , Yaomei Wang , Yumin Huang , Chengjie Gao , Xinhua Guo , Lixiang Chen , Huizhi Zhao , Xiuli An

The fetal liver (FL) is the key erythropoietic organ during fetal development, but knowledge on human FL erythropoiesis is very limited. In this study, we sorted primary erythroblasts from FL cells and performed RNA sequencing (RNA-seq) analyses. We found that temporal gene expression patterns reflected changes in function during primary human FL terminal erythropoiesis. Notably, the expression of genes enriched in proteolysis and autophagy was up-regulated in orthochromatic erythroblasts (OrthoEs), suggesting the involvement of these pathways in enucleation. We also performed RNA-seq of in vitro cultured erythroblasts derived from FL CD34⁺ cells. Comparison of transcriptomes between the primary and cultured erythroblasts revealed significant differences, indicating impacts of the culture system on gene expression. Notably, the expression of lipid metabolism-related genes was increased in cultured erythroblasts. We further immortalized erythroid cell lines from FL and cord blood (CB) CD34⁺ cells (FL-iEry and CB-iEry, respectively). FL-iEry and CB-iEry were immortalized at the proerythroblast stage and can be induced to differentiate into OrthoEs, but their enucleation ability was very low. Comparison of the transcriptomes between OrthoEs with and without enucleation capability revealed the down-regulation of pathways involved in chromatin organization and mitophagy in OrthoEs without enucleation capacity, indicating that defects in chromatin organization and mitophagy contribute to the inability of OrthoEs to enucleate. Additionally, the expression of HBE1, HBZ, and HBG2 was up-regulated in FL-iEry compared with CB-iEry, and such up-regulation was accompanied by down-regulated expression of BCL11A and up-regulated expression of LIN28B and IGF2BP1. Our study provides new insights into human FL erythropoiesis and rich resources for future studies.

胎儿肝脏（FL）是胎儿发育过程中关键的红细胞生成器官，但有关人类FL红细胞生成的知识却非常有限。在这项研究中，我们从FL细胞中分拣出原代红细胞，并进行了RNA测序（RNA-seq）分析。我们发现，时间基因表达模式反映了原代人类 FL 终末红细胞生成过程中的功能变化。值得注意的是，在正色红细胞（OrthoEs）中，富含蛋白分解和自噬的基因表达上调，这表明这些通路参与了去核过程。我们还对从FL CD34+细胞中提取的体外培养红细胞进行了RNA-seq分析。比较原代红细胞和培养红细胞的转录组发现了显著差异，表明培养系统对基因表达有影响。值得注意的是，脂质代谢相关基因的表达在培养红细胞中有所增加。我们进一步从 FL 和脐带血（CB）CD34+细胞中永生化了红细胞系（分别为 FL-iEry 和 CB-iEry）。FL-iEry和CB-iEry在原红细胞阶段永生，可诱导分化成OrthoEs，但它们的去核能力很低。比较具有和不具有去核能力的OrthoEs的转录组发现，在不具有去核能力的OrthoEs中，参与染色质组织和有丝分裂的通路下调，这表明染色质组织和有丝分裂的缺陷导致OrthoEs不能去核。此外，与 CB-iEry 相比，FL-iEry 中 HBE1、HBZ 和 HBG2 的表达上调，这种上调伴随着 BCL11A 的表达下调以及 LIN28B 和 IGF2BP1 的表达上调。我们的研究为人类 FL 红细胞生成提供了新的见解，并为今后的研究提供了丰富的资源。

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引用次数: 0

Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing 与 SpCas9 相比，SaCas9 在基因组编辑中具有更高的保真度和不同的编辑结果。

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-12-01 DOI: 10.1016/j.gpb.2022.12.003

Zhi-Xue Yang , Ya-Wen Fu , Juan-Juan Zhao , Feng Zhang , Si-Ang Li , Mei Zhao , Wei Wen , Lei Zhang , Tao Cheng , Jian-Ping Zhang , Xiao-Bing Zhang

A series of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 (Cas9) systems have been engineered for genome editing. The most widely used Cas9 is SpCas9 from Streptococcus pyogenes and SaCas9 from Staphylococcus aureus. However, a comparison of their detailed gene editing outcomes is still lacking. By characterizing the editing outcomes of 11 sites in human induced pluripotent stem cells (iPSCs) and K562 cells, we found that SaCas9 could edit the genome with greater efficiencies than SpCas9. We also compared the effects of spacer lengths of single-guide RNAs (sgRNAs; 18–21 nt for SpCas9 and 19–23 nt for SaCas9) and found that the optimal spacer lengths were 20 nt and 21 nt for SpCas9 and SaCas9, respectively. However, the optimal spacer length for a particular sgRNA was 18–21 nt for SpCas9 and 21–22 nt for SaCas9. Furthermore, SpCas9 exhibited a more substantial bias than SaCas9 for nonhomologous end-joining (NHEJ) +1 insertion at the fourth nucleotide upstream of the protospacer adjacent motif (PAM), indicating a characteristic of a staggered cut. Accordingly, editing with SaCas9 led to higher efficiencies of NHEJ-mediated double-stranded oligodeoxynucleotide (dsODN) insertion or homology-directed repair (HDR)-mediated adeno-associated virus serotype 6 (AAV6) donor knock-in. Finally, GUIDE-seq analysis revealed that SaCas9 exhibited significantly reduced off-target effects compared with SpCas9. Our work indicates the superior performance of SaCas9 to SpCas9 in transgene integration-based therapeutic gene editing and the necessity to identify the optimal spacer length to achieve desired editing results.

目前已设计出一系列用于基因组编辑的簇状规则间隔短回文重复序列（CRISPR）-CRISPR 相关蛋白 9（Cas9）系统。使用最广泛的 Cas9 是来自化脓性链球菌的 SpCas9 和来自金黄色葡萄球菌的 SaCas9。然而，目前仍缺乏对其基因编辑结果的详细比较。通过分析人类诱导多能干细胞（iPSC）和 K562 细胞中 11 个位点的编辑结果，我们发现 SaCas9 比 SpCas9 能更有效地编辑基因组。我们还比较了单导RNA（sgRNA，SpCas9为18-21 nt，SaCas9为19-23 nt）的间隔长度，发现SpCas9和SaCas9的最佳间隔长度分别为20 nt和21 nt。然而，对于 SpCas9 和 SaCas9 而言，特定引导 RNA 的最佳间隔长度分别为 18-21 nt 或 21-22 nt。此外，与 SaCas9 相比，SpCas9 在非同源末端连接（NHEJ）+1 插入原间隔邻接基序（PAM）上游第四个核苷酸时表现出更大的偏差，这是交错切割的特征。因此，用SaCas9进行编辑可提高NHEJ介导的双链寡核苷酸（dsODN）插入或腺病毒血清型6（AAV6）供体介导的同源定向修复（HDR）的基因敲入效率。最后，GUIDE-seq分析显示，与SpCas9相比，SaCas9的脱靶效应明显降低。我们的工作表明，在基于转基因整合的治疗性基因编辑中，SaCas9的性能优于SpCas9，而且有必要确定最佳间隔长度，以实现理想的编辑效果。

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引用次数: 0

Cancer Is A Survival Process under Persistent Microenvironmental and Cellular Stresses 癌症是在持续的微环境和细胞压力下的生存过程。

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-12-01 DOI: 10.1016/j.gpb.2022.03.002

Renbo Tan , Yi Zhou , Zheng An , Ying Xu

引用次数: 0

Acid–base Homeostasis and Implications to the Phenotypic Behaviors of Cancer 酸碱平衡及其对癌症表型行为的影响

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-12-01 DOI: 10.1016/j.gpb.2022.06.003

Yi Zhou , Wennan Chang , Xiaoyu Lu , Jin Wang , Chi Zhang , Ying Xu

Acid–base homeostasis is a fundamental property of living cells, and its persistent disruption in human cells can lead to a wide range of diseases. In this study, we conducted a computational modeling analysis of transcriptomic data of 4750 human tissue samples of 9 cancer types in The Cancer Genome Atlas (TCGA) database. Built on our previous study, we quantitatively estimated the average production rate of OH⁻ by cytosolic Fenton reactions, which continuously disrupt the intracellular pH (pH_i) homeostasis. Our predictions indicate that all or at least a subset of 43 reprogrammed metabolisms (RMs) are induced to produce net protons (H⁺) at comparable rates of Fenton reactions to keep the pH_i stable. We then discovered that a number of well-known phenotypes of cancers, including increased growth rate, metastasis rate, and local immune cell composition, can be naturally explained in terms of the Fenton reaction level and the induced RMs. This study strongly suggests the possibility to have a unified framework for studies of cancer-inducing stressors, adaptive metabolic reprogramming, and cancerous behaviors. In addition, strong evidence is provided to demonstrate that a popular view that Na⁺/H⁺ exchangers along with lactic acid exporters and carbonic anhydrases are responsible for the intracellular alkalization and extracellular acidification in cancer may not be justified.

酸碱平衡是活细胞的基本特性，人类细胞中酸碱平衡的持续破坏会导致多种疾病。我们对癌症基因组图谱（TCGA）数据库中九种癌症类型的 4750 份人体组织样本的转录组数据进行了计算建模和分析。在之前研究的基础上，我们对持续破坏细胞内 pH 平衡的细胞膜芬顿反应产生 OH- 的（平均）速率进行了定量估算。我们的预测表明，43 种重编程代谢物（RMs）中的全部或一部分都会被诱导以相当的芬顿反应速率产生净质子（H+），以保持细胞内 pH 值的稳定。我们随后发现，一些众所周知的癌症表型，包括生长率、转移率和局部免疫细胞组成的增加，都可以用芬顿反应水平和诱导的 RMs 来自然地解释。这项研究有力地表明，有可能为癌症诱导应激源、适应性代谢重编程和癌症行为的研究建立一个统一的框架。此外，该研究还提供了有力的证据，证明了Na+/H+交换体与乳酸输出体和碳酸酐酶共同负责癌症细胞内碱化和细胞外酸化的普遍观点可能是不正确的。

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引用次数: 0

GREPore-seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-range PCR and Nanopore Sequencing GREPore-seq：通过长程 PCR 和纳米孔测序检测基因编辑后变化的强大工作流程。

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-12-01 DOI: 10.1016/j.gpb.2022.06.002

Zi-Jun Quan , Si-Ang Li , Zhi-Xue Yang , Juan-Juan Zhao , Guo-Hua Li , Feng Zhang , Wei Wen , Tao Cheng , Xiao-Bing Zhang

To achieve the enormous potential of gene-editing technology in clinical therapies, one needs to evaluate both the on-target efficiency and unintended editing consequences comprehensively. However, there is a lack of a pipelined, large-scale, and economical workflow for detecting genome editing outcomes, in particular insertion or deletion of a large fragment. Here, we describe an approach for efficient and accurate detection of multiple genetic changes after CRISPR/Cas9 editing by pooled nanopore sequencing of barcoded long-range PCR products. Recognizing the high error rates of Oxford nanopore sequencing, we developed a novel pipeline to capture the barcoded sequences by grepping reads of nanopore amplicon sequencing (GREPore-seq). GREPore-seq can assess nonhomologous end-joining (NHEJ)-mediated double-stranded oligodeoxynucleotide (dsODN) insertions with comparable accuracy to Illumina next-generation sequencing (NGS). GREPore-seq also reveals a full spectrum of homology-directed repair (HDR)-mediated large gene knock-in, correlating well with the fluorescence-activated cell sorting (FACS) analysis results. Of note, we discovered low-level fragmented and full-length plasmid backbone insertion at the CRISPR cutting site. Therefore, we have established a practical workflow to evaluate various genetic changes, including quantifying insertions of short dsODNs, knock-ins of long pieces, plasmid insertions, and large fragment deletions after CRISPR/Cas9-mediated editing. GREPore-seq is freely available at GitHub (https://github.com/lisiang/GREPore-seq) and the National Genomics Data Center (NGDC) BioCode (https://ngdc.cncb.ac.cn/biocode/tools/BT007293).

为了发挥基因编辑技术在临床治疗中的巨大潜力，我们需要全面评估靶向效率和意外编辑后果。然而，目前还缺乏一种流水线式、大规模且经济的工作流程来检测基因组编辑结果，尤其是大片段的插入或缺失。在这里，我们介绍了一种通过对条形码长程 PCR 产物进行集合纳米孔测序，高效准确地检测 CRISPR/Cas9 编辑后多种基因变化的方法。由于认识到牛津纳米孔测序的高错误率，我们开发了一种新型管道，通过对纳米孔扩增子测序的读数进行抓取（GREPore-seq）来捕获条形码序列。GREPore-seq 可以评估非同源末端连接（NHEJ）介导的双链寡脱氧核苷酸（dsODN）插入，其准确性与 Illumina 下一代测序（NGS）相当。GREPore-seq 还揭示了同源定向修复（HDR）介导的大基因敲入的全谱，与荧光激活细胞分选（FACS）分析结果密切相关。值得注意的是，我们在 CRISPR 切割位点发现了低水平的片段和全长质粒骨架插入。因此，我们建立了一套实用的工作流程来评估各种基因变化，包括量化 CRISPR 编辑后的短 dsODNs 插入、长片段敲入、质粒插入和大片段缺失。GREPore-seq可在GitHub（https://github.com/lisiang/GREPore-seq）和美国国家基因组学数据中心（NGDC）生物代码（https://ngdc.cncb.ac.cn/biocode/tools/BT007293）上免费获取。

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引用次数: 0

Protein Lactylation and Metabolic Regulation of the Zoonotic Parasite Toxoplasma gondii 人畜共患病寄生虫弓形虫的蛋白质乳化和代谢调节。

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-12-01 DOI: 10.1016/j.gpb.2022.09.010

Deqi Yin , Ning Jiang , Chang Cheng , Xiaoyu Sang , Ying Feng , Ran Chen , Qijun Chen

The biology of Toxoplasma gondii, the causative pathogen of one of the most widespread parasitic diseases (toxoplasmosis), remains poorly understood. Lactate, which is derived from glucose metabolism, is not only an energy source in a variety of organisms, including T. gondii, but also a regulatory molecule that participates in gene activation and protein function. Lysine lactylation (Kla) is a type of post-translational modifications (PTMs) that has been recently associated with chromatin remodeling; however, Kla of histone and non-histone proteins has not yet been studied in T. gondii. To examine the prevalence and function of lactylation in T. gondii parasites, we mapped the lactylome of proliferating tachyzoite cells and identified 1964 Kla sites on 955 proteins in the T. gondii RH strain. Lactylated proteins were distributed in multiple subcellular compartments and were closely related to a wide variety of biological processes, including mRNA splicing, glycolysis, aminoacyl-tRNA biosynthesis, RNA transport, and many signaling pathways. We also performed a chromatin immunoprecipitation sequencing (ChIP-seq) analysis using a lactylation-specific antibody and found that the histones H4K12la and H3K14la were enriched in the promoter and exon regions of T. gondii associated with microtubule-based movement and cell invasion. We further confirmed the delactylase activity of histone deacetylases TgHDAC2–4, and found that treatment with anti-histone acetyltransferase (TgMYST-A) antibodies profoundly reduced protein lactylation in T. gondii. This study offers the first dataset of the global lactylation proteome and provides a basis for further dissecting the functional biology of T. gondii.

弓形虫是最普遍的寄生虫病之一（弓形虫病）的致病病原体，但人们对弓形虫的生物学特性仍然知之甚少。葡萄糖代谢产生的乳酸不仅是包括弓形虫在内的多种生物的能量来源，也是参与基因激活和蛋白质功能的调节分子。赖氨酸乳化（Kla）是一种翻译后修饰（PTM），最近被认为与染色质重塑有关。为了研究乳化作用在淋病双球菌寄生虫中的普遍性和功能，我们绘制了增殖速虫细胞的乳化组图谱，并在淋病双球菌 RH 株的 955 个蛋白质上鉴定出了 1964 个乳化位点。乳化蛋白分布在多个亚细胞区，与多种生物过程密切相关，包括 mRNA 剪接、糖酵解、氨基酰-tRNA 生物合成、RNA 运输和许多信号通路。我们还使用乳化特异性抗体进行了染色质免疫沉淀测序（ChIP-seq）分析，发现组蛋白H4K12la和H3K14la富集在与微管运动和细胞侵袭相关的淋球菌启动子和外显子区域。我们进一步证实了组蛋白去乙酰化酶 TgHDACs 2、3 和 4 的脱乳活性，并发现用抗组蛋白乙酰转移酶（TgMYST-A）抗体处理能显著减少淋病双球菌的蛋白乳化。这项研究首次提供了全球乳化蛋白质组的数据集，为进一步剖析淋球菌的功能生物学提供了基础。

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引用次数: 0