发布求助
文献互助 智能选刊 最新文献

Annual review of biochemistry最新文献

筛选
英文 中文
Mitochondrial DNA Release in Innate Immune Signaling. 先天性免疫信号中的线粒体 DNA 释放
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 Epub Date: 2023-03-31 DOI: 10.1146/annurev-biochem-032620-104401
Laura E Newman, Gerald S Shadel
{"title":"Mitochondrial DNA Release in Innate Immune Signaling.","authors":"Laura E Newman, Gerald S Shadel","doi":"10.1146/annurev-biochem-032620-104401","DOIUrl":"10.1146/annurev-biochem-032620-104401","url":null,"abstract":"<p><p>According to the endosymbiotic theory, most of the DNA of the original bacterial endosymbiont has been lost or transferred to the nucleus, leaving a much smaller (∼16 kb in mammals), circular molecule that is the present-day mitochondrial DNA (mtDNA). The ability of mtDNA to escape mitochondria and integrate into the nuclear genome was discovered in budding yeast, along with genes that regulate this process. Mitochondria have emerged as key regulators of innate immunity, and it is now recognized that mtDNA released into the cytoplasm, outside of the cell, or into circulation activates multiple innate immune signaling pathways. Here, we first review the mechanisms through which mtDNA is released into the cytoplasm, including several inducible mitochondrial pores and defective mitophagy or autophagy. Next, we cover how the different forms of released mtDNA activate specific innate immune nucleic acid sensors and inflammasomes. Finally, we discuss how intracellular and extracellular mtDNA release, including circulating cell-free mtDNA that promotes systemic inflammation, are implicated in human diseases, bacterial and viral infections, senescence and aging.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"299-332"},"PeriodicalIF":12.1,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11058562/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9662511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Rubisco Function, Evolution, and Engineering. Rubisco功能，进化和工程。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 DOI: 10.1146/annurev-biochem-040320-101244
Noam Prywes, Naiya R Phillips, Owen T Tuck, Luis E Valentin-Alvarado, David F Savage
{"title":"Rubisco Function, Evolution, and Engineering.","authors":"Noam Prywes,&nbsp;Naiya R Phillips,&nbsp;Owen T Tuck,&nbsp;Luis E Valentin-Alvarado,&nbsp;David F Savage","doi":"10.1146/annurev-biochem-040320-101244","DOIUrl":"https://doi.org/10.1146/annurev-biochem-040320-101244","url":null,"abstract":"<p><p>Carbon fixation is the process by which CO<sub>2</sub> is converted from a gas into biomass. The Calvin-Benson-Bassham cycle (CBB) is the dominant carbon-consuming pathway on Earth, driving >99.5% of the ∼120 billion tons of carbon that are converted to sugar by plants, algae, and cyanobacteria. The carboxylase enzyme in the CBB, ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco), fixes one CO<sub>2</sub> molecule per turn of the cycle into bioavailable sugars. Despite being critical to the assimilation of carbon, rubisco's kinetic rate is not very fast, limiting flux through the pathway. This bottleneck presents a paradox: Why has rubisco not evolved to be a better catalyst? Many hypothesize that the catalytic mechanism of rubisco is subject to one or more trade-offs and that rubisco variants have been optimized for their native physiological environment. Here, we review the evolution and biochemistry of rubisco through the lens of structure and mechanism in order to understand what trade-offs limit its improvement. We also review the many attempts to improve rubisco itself and thereby promote plant growth.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"385-410"},"PeriodicalIF":16.6,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9670773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
DNA Fragility and Repair: Some Personal Recollections. DNA的脆弱和修复:一些个人回忆。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 DOI: 10.1146/annurev-biochem-071322-020214
Tomas Robert Lindahl
{"title":"DNA Fragility and Repair: Some Personal Recollections.","authors":"Tomas Robert Lindahl","doi":"10.1146/annurev-biochem-071322-020214","DOIUrl":"https://doi.org/10.1146/annurev-biochem-071322-020214","url":null,"abstract":"<p><p>In this autobiographical article, I reflect on my Swedish background. Then I discuss endogenous DNA alterations and the base excision repair pathway and alternative repair strategies for some unusual DNA lesions. Endogenous DNA damage, such as loss of purine bases and cytosine deamination, is proposed as a major source of cancer-causing mutations.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"1-13"},"PeriodicalIF":16.6,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9662514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
mRNA Regulation by RNA Modifications. 通过 RNA 修饰调节 mRNA。
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 Epub Date: 2023-04-05 DOI: 10.1146/annurev-biochem-052521-035949
Wendy V Gilbert, Sigrid Nachtergaele
{"title":"mRNA Regulation by RNA Modifications.","authors":"Wendy V Gilbert, Sigrid Nachtergaele","doi":"10.1146/annurev-biochem-052521-035949","DOIUrl":"10.1146/annurev-biochem-052521-035949","url":null,"abstract":"<p><p>Chemical modifications on mRNA represent a critical layer of gene expression regulation. Research in this area has continued to accelerate over the last decade, as more modifications are being characterized with increasing depth and breadth. mRNA modifications have been demonstrated to influence nearly every step from the early phases of transcript synthesis in the nucleus through to their decay in the cytoplasm, but in many cases, the molecular mechanisms involved in these processes remain mysterious. Here, we highlight recent work that has elucidated the roles of mRNA modifications throughout the mRNA life cycle, describe gaps in our understanding and remaining open questions, and offer some forward-looking perspective on future directions in the field.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"175-198"},"PeriodicalIF":12.1,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11192554/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9662525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Looping the Genome with SMC Complexes. 用SMC复合物环化基因组。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 DOI: 10.1146/annurev-biochem-032620-110506
Eugene Kim, Roman Barth, Cees Dekker
{"title":"Looping the Genome with SMC Complexes.","authors":"Eugene Kim,&nbsp;Roman Barth,&nbsp;Cees Dekker","doi":"10.1146/annurev-biochem-032620-110506","DOIUrl":"https://doi.org/10.1146/annurev-biochem-032620-110506","url":null,"abstract":"<p><p>SMC (structural maintenance of chromosomes) protein complexes are an evolutionarily conserved family of motor proteins that hold sister chromatids together and fold genomes throughout the cell cycle by DNA loop extrusion. These complexes play a key role in a variety of functions in the packaging and regulation of chromosomes, and they have been intensely studied in recent years. Despite their importance, the detailed molecular mechanism for DNA loop extrusion by SMC complexes remains unresolved. Here, we describe the roles of SMCs in chromosome biology and particularly review in vitro single-molecule studies that have recently advanced our understanding of SMC proteins. We describe the mechanistic biophysical aspects of loop extrusion that govern genome organization and its consequences.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"15-41"},"PeriodicalIF":16.6,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9725135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
The Design and Application of DNA-Editing Enzymes as Base Editors. 作为碱基编辑器的 DNA 编辑酶的设计与应用。
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 Epub Date: 2023-04-05 DOI: 10.1146/annurev-biochem-052521-013938
Kartik L Rallapalli, Alexis C Komor
{"title":"The Design and Application of DNA-Editing Enzymes as Base Editors.","authors":"Kartik L Rallapalli, Alexis C Komor","doi":"10.1146/annurev-biochem-052521-013938","DOIUrl":"10.1146/annurev-biochem-052521-013938","url":null,"abstract":"<p><p>DNA-editing enzymes perform chemical reactions on DNA nucleobases. These reactions can change the genetic identity of the modified base or modulate gene expression. Interest in DNA-editing enzymes has burgeoned in recent years due to the advent of clustered regularly interspaced short palindromic repeat-associated (CRISPR-Cas) systems, which can be used to direct their DNA-editing activity to specific genomic loci of interest. In this review, we showcase DNA-editing enzymes that have been repurposed or redesigned and developed into programmable base editors. These include deaminases, glycosylases, methyltransferases, and demethylases. We highlight the astounding degree to which these enzymes have been redesigned, evolved, and refined and present these collective engineering efforts as a paragon for future efforts to repurpose and engineer other families of enzymes. Collectively, base editors derived from these DNA-editing enzymes facilitate programmable point mutation introduction and gene expression modulation by targeted chemical modification of nucleobases.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"43-79"},"PeriodicalIF":12.1,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10330504/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9756297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Inseparable Relationship Between Cholesterol and Hedgehog Signaling. 胆固醇与刺猬信号之间密不可分的关系
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 Epub Date: 2023-03-31 DOI: 10.1146/annurev-biochem-052521-040313
Christian Siebold, Rajat Rohatgi
{"title":"The Inseparable Relationship Between Cholesterol and Hedgehog Signaling.","authors":"Christian Siebold, Rajat Rohatgi","doi":"10.1146/annurev-biochem-052521-040313","DOIUrl":"10.1146/annurev-biochem-052521-040313","url":null,"abstract":"<p><p>Ligands of the Hedgehog (HH) pathway are paracrine signaling molecules that coordinate tissue development in metazoans. A remarkable feature of HH signaling is the repeated use of cholesterol in steps spanning ligand biogenesis, secretion, dispersal, and reception on target cells. A cholesterol molecule covalently attached to HH ligands is used as a molecular baton by transfer proteins to guide their secretion, spread, and reception. On target cells, a signaling circuit composed of a cholesterol transporter and sensor regulates transmission of HH signals across the plasma membrane to the cytoplasm. The repeated use of cholesterol in signaling supports the view that the HH pathway likely evolved by coopting ancient systems to regulate the abundance or organization of sterol-like lipids in membranes.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"273-298"},"PeriodicalIF":12.1,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10330520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9769873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Activation Mechanism of the Insulin Receptor: A Structural Perspective. 胰岛素受体的激活机制:一个结构视角。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 DOI: 10.1146/annurev-biochem-052521-033250
Eunhee Choi, Xiao-Chen Bai
{"title":"The Activation Mechanism of the Insulin Receptor: A Structural Perspective.","authors":"Eunhee Choi,&nbsp;Xiao-Chen Bai","doi":"10.1146/annurev-biochem-052521-033250","DOIUrl":"https://doi.org/10.1146/annurev-biochem-052521-033250","url":null,"abstract":"<p><p>The insulin receptor (IR) is a type II receptor tyrosine kinase that plays essential roles in metabolism, growth, and proliferation. Dysregulation of IR signaling is linked to many human diseases, such as diabetes and cancers. The resolution revolution in cryo-electron microscopy has led to the determination of several structures of IR with different numbers of bound insulin molecules in recent years, which have tremendously improved our understanding of how IR is activated by insulin. Here, we review the insulin-induced activation mechanism of IR, including (<i>a</i>) the detailed binding modes and functions of insulin at site 1 and site 2 and (<i>b</i>) the insulin-induced structural transitions that are required for IR activation. We highlight several other key aspects of the activation and regulation of IR signaling and discuss the remaining gaps in our understanding of the IR activation mechanism and potential avenues of future research.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"247-272"},"PeriodicalIF":16.6,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10398885/pdf/nihms-1919378.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9929688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
The Proteins of mRNA Modification: Writers, Readers, and Erasers. mRNA修饰的蛋白质:写入器，读取器和擦除器。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 DOI: 10.1146/annurev-biochem-052521-035330
Mathieu N Flamand, Matthew Tegowski, Kate D Meyer
{"title":"The Proteins of mRNA Modification: Writers, Readers, and Erasers.","authors":"Mathieu N Flamand,&nbsp;Matthew Tegowski,&nbsp;Kate D Meyer","doi":"10.1146/annurev-biochem-052521-035330","DOIUrl":"https://doi.org/10.1146/annurev-biochem-052521-035330","url":null,"abstract":"<p><p>Over the past decade, mRNA modifications have emerged as important regulators of gene expression control in cells. Fueled in large part by the development of tools for detecting RNA modifications transcriptome wide, researchers have uncovered a diverse epitranscriptome that serves as an additional layer of gene regulation beyond simple RNA sequence. Here, we review the proteins that write, read, and erase these marks, with a particular focus on the most abundant internal modification, <i>N</i><sup>6</sup>-methyladenosine (m<sup>6</sup>A). We first describe the discovery of the key enzymes that deposit and remove m<sup>6</sup>A and other modifications and discuss how our understanding of these proteins has shaped our views of modification dynamics. We then review current models for the function of m<sup>6</sup>A reader proteins and how our knowledge of these proteins has evolved. Finally, we highlight important future directions for the field and discuss key questions that remain unanswered.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"145-173"},"PeriodicalIF":16.6,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10443600/pdf/nihms-1922506.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10042992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 14
Polyamines in Parkinson's Disease: Balancing Between Neurotoxicity and Neuroprotection. 帕金森病中的多胺:神经毒性和神经保护之间的平衡。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2023-06-20 DOI: 10.1146/annurev-biochem-071322-021330
Stephanie Vrijsen, Marine Houdou, Ana Cascalho, Jan Eggermont, Peter Vangheluwe
{"title":"Polyamines in Parkinson's Disease: Balancing Between Neurotoxicity and Neuroprotection.","authors":"Stephanie Vrijsen,&nbsp;Marine Houdou,&nbsp;Ana Cascalho,&nbsp;Jan Eggermont,&nbsp;Peter Vangheluwe","doi":"10.1146/annurev-biochem-071322-021330","DOIUrl":"https://doi.org/10.1146/annurev-biochem-071322-021330","url":null,"abstract":"<p><p>The polyamines putrescine, spermidine, and spermine are abundant polycations of vital importance in mammalian cells. Their cellular levels are tightly regulated by degradation and synthesis, as well as by uptake and export. Here, we discuss the delicate balance between the neuroprotective and neurotoxic effects of polyamines in the context of Parkinson's disease (PD). Polyamine levels decline with aging and are altered in patients with PD, whereas recent mechanistic studies on ATP13A2 (PARK9) demonstrated a driving role of a disturbed polyamine homeostasis in PD. Polyamines affect pathways in PD pathogenesis, such as α-synuclein aggregation, and influence PD-related processes like autophagy, heavy metal toxicity, oxidative stress, neuroinflammation, and lysosomal/mitochondrial dysfunction. We formulate outstanding research questions regarding the role of polyamines in PD, their potential as PD biomarkers, and possible therapeutic strategies for PD targeting polyamine homeostasis.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"92 ","pages":"435-464"},"PeriodicalIF":16.6,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9662523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
首页 上一页 下一页 尾页
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整，为了账户安全，请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们：info@booksci.cn Book学术提供免费学术资源搜索服务，方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号：481959085
Book学术官方微信