Pub Date : 2022-08-01Epub Date: 2022-08-23DOI: 10.1042/bio_2022_119
Ram Prosad Chakrabarty, Navdeep S Chandel
Mitochondria, special double-membraned intracellular compartments or 'organelles', are popularly known as the 'powerhouses of the cell', as they generate the bulk of ATP used to fuel cellular biochemical reactions. Mitochondria are also well known for generating metabolites for the synthesis of macromolecules (e.g., carbohydrates, proteins, lipids and nucleic acids). In the mid-1990s, new evidence suggesting that mitochondria, beyond their canonical roles in bioenergetics and biosynthesis, can act as signalling organelles began to emerge, bringing a dramatic shift in our view of mitochondria's roles in controlling cell function. Over the next two and half decades, works from multiple groups have demonstrated how mitochondrial signalling can dictate diverse physiological and pathophysiological outcomes. In this article, we will briefly discuss different mechanisms by which mitochondria can communicate with cytosol and other organelles to regulate cell fate and function and exert paracrine effects. Our molecular understanding of mitochondrial communication with the rest of the cell, i.e. mitochondrial signalling, could reveal new therapeutic strategies to improve health and ameliorate diseases.
线粒体是一种特殊的双膜式细胞内隔室或 "细胞器"，被人们称为 "细胞的动力室"，因为它们产生的大部分 ATP 都用于促进细胞的生化反应。众所周知，线粒体还能产生合成大分子（如碳水化合物、蛋白质、脂类和核酸）的代谢物。20 世纪 90 年代中期，有新证据表明线粒体除了在生物能和生物合成方面发挥传统作用外，还可以作为信号细胞器发挥作用，这使我们对线粒体在控制细胞功能方面的作用的看法发生了巨大转变。在接下来的二十五年中，多个研究小组的工作证明了线粒体信号如何决定各种生理和病理生理结果。在本文中，我们将简要讨论线粒体与细胞质和其他细胞器沟通以调控细胞命运和功能并发挥旁分泌效应的不同机制。我们对线粒体与细胞其他部分交流的分子理解，即线粒体信号，可以揭示改善健康和疾病的新治疗策略。
{"title":"Beyond ATP, new roles of mitochondria.","authors":"Ram Prosad Chakrabarty, Navdeep S Chandel","doi":"10.1042/bio_2022_119","DOIUrl":"10.1042/bio_2022_119","url":null,"abstract":"<p><p>Mitochondria, special double-membraned intracellular compartments or 'organelles', are popularly known as the 'powerhouses of the cell', as they generate the bulk of ATP used to fuel cellular biochemical reactions. Mitochondria are also well known for generating metabolites for the synthesis of macromolecules (e.g., carbohydrates, proteins, lipids and nucleic acids). In the mid-1990s, new evidence suggesting that mitochondria, beyond their canonical roles in bioenergetics and biosynthesis, can act as signalling organelles began to emerge, bringing a dramatic shift in our view of mitochondria's roles in controlling cell function. Over the next two and half decades, works from multiple groups have demonstrated how mitochondrial signalling can dictate diverse physiological and pathophysiological outcomes. In this article, we will briefly discuss different mechanisms by which mitochondria can communicate with cytosol and other organelles to regulate cell fate and function and exert paracrine effects. Our molecular understanding of mitochondrial communication with the rest of the cell, i.e. mitochondrial signalling, could reveal new therapeutic strategies to improve health and ameliorate diseases.</p>","PeriodicalId":35334,"journal":{"name":"Biochemist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9558425/pdf/nihms-1839106.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10054062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mitochondria are complex factories that provide our cells with most of the energy we need to survive and perform daily tasks. They comprise their own small genome, mitochondrial DNA (mtDNA), which contains genes for parts of the energy-producing machinery. Mutations in mtDNA can lead to mitochondrial diseases, which are a devastating group of heterogenous inheritable diseases that can develop at any stage of life. Despite rapid developments in genome engineering for nuclear DNA, the incompatibility of certain techniques in mitochondria has meant that the field of mitochondrial genome modification has been impeded for many years. However, recent advances in mtDNA engineering techniques, such as programmable nucleases and base editors, will allow for a deeper understanding of the processes taking place in mitochondria and improve the prospects of developing treatments for mitochondrial diseases.
{"title":"Fixing the powerhouse: genetic engineering of mitochondrial DNA","authors":"C. Mutti, Pedro Silva-Pinheiro, M. Minczuk","doi":"10.1042/bio_2022_120","DOIUrl":"https://doi.org/10.1042/bio_2022_120","url":null,"abstract":"Mitochondria are complex factories that provide our cells with most of the energy we need to survive and perform daily tasks. They comprise their own small genome, mitochondrial DNA (mtDNA), which contains genes for parts of the energy-producing machinery. Mutations in mtDNA can lead to mitochondrial diseases, which are a devastating group of heterogenous inheritable diseases that can develop at any stage of life. Despite rapid developments in genome engineering for nuclear DNA, the incompatibility of certain techniques in mitochondria has meant that the field of mitochondrial genome modification has been impeded for many years. However, recent advances in mtDNA engineering techniques, such as programmable nucleases and base editors, will allow for a deeper understanding of the processes taking place in mitochondria and improve the prospects of developing treatments for mitochondrial diseases.","PeriodicalId":35334,"journal":{"name":"Biochemist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41771714","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}
{"title":"Sustainability in biochemistry","authors":"Heather Doran","doi":"10.1042/bio_2022_117","DOIUrl":"https://doi.org/10.1042/bio_2022_117","url":null,"abstract":"","PeriodicalId":35334,"journal":{"name":"Biochemist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48460695","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 use of enzymes (protein catalysts from biological origin) has been key to the development of our society and daily life since the dawn of humanity. Nowadays, the better understanding of how enzymes work and their manipulation has enabled enzymes to become a crucial technology in the current biotechnological revolution. In this sense, while enzymes in their naturally occurring form are excellent biocatalysts, they are not yet broadly implemented in industry due to their instability and poor reusability. As a solution, enzyme immobilization is a strategy that enables the preparation of more resistant, reusable and more cost-efficient biocatalysts that, combined with continuous flow technologies, have the potential to make their promise true: transition towards more cost-efficient, sustainable, and environmental friendly chemical manufacturing.
{"title":"Back to the future: taking enzymes to the next level of sustainability","authors":"D. R. Padrosa, Ana I. Benítez-Mateos, F. Paradisi","doi":"10.1042/bio_2022_109","DOIUrl":"https://doi.org/10.1042/bio_2022_109","url":null,"abstract":"The use of enzymes (protein catalysts from biological origin) has been key to the development of our society and daily life since the dawn of humanity. Nowadays, the better understanding of how enzymes work and their manipulation has enabled enzymes to become a crucial technology in the current biotechnological revolution. In this sense, while enzymes in their naturally occurring form are excellent biocatalysts, they are not yet broadly implemented in industry due to their instability and poor reusability. As a solution, enzyme immobilization is a strategy that enables the preparation of more resistant, reusable and more cost-efficient biocatalysts that, combined with continuous flow technologies, have the potential to make their promise true: transition towards more cost-efficient, sustainable, and environmental friendly chemical manufacturing.","PeriodicalId":35334,"journal":{"name":"Biochemist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46261933","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}
Enzymes are the catalytically active proteins, responsible for carrying out biochemistry in nature. Today, they are also finding use as catalysts in organic chemistry, both in the laboratory as well as in large-scale manufacturing of chemicals in industry. Their special properties enable sustainable syntheses, supported by tools such as protein engineering so they can be tuned to operate efficiently, thereby meeting industrial requirements.
{"title":"Biocatalysis for future sustainable manufacturing","authors":"J. Woodley","doi":"10.1042/bio_2022_112","DOIUrl":"https://doi.org/10.1042/bio_2022_112","url":null,"abstract":"Enzymes are the catalytically active proteins, responsible for carrying out biochemistry in nature. Today, they are also finding use as catalysts in organic chemistry, both in the laboratory as well as in large-scale manufacturing of chemicals in industry. Their special properties enable sustainable syntheses, supported by tools such as protein engineering so they can be tuned to operate efficiently, thereby meeting industrial requirements.","PeriodicalId":35334,"journal":{"name":"Biochemist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46590301","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}
Farmed animal agriculture is facing big challenges in today’s world. Genome editing technology now offers some solutions, and these need to be melded into the other approaches and strategies that can be deployed to produce a sustainable food system. If we embrace these technologies, and do so within a basic justice framing, we can achieve food security for all, while providing enhanced welfare and reduced environmental footprint contributing to a fair and sustainable carbon-zero future.
{"title":"Increasing livestock farming sustainability using genome editing technology","authors":"B. Whitelaw, S. Lillico","doi":"10.1042/bio_2022_114","DOIUrl":"https://doi.org/10.1042/bio_2022_114","url":null,"abstract":"Farmed animal agriculture is facing big challenges in today’s world. Genome editing technology now offers some solutions, and these need to be melded into the other approaches and strategies that can be deployed to produce a sustainable food system. If we embrace these technologies, and do so within a basic justice framing, we can achieve food security for all, while providing enhanced welfare and reduced environmental footprint contributing to a fair and sustainable carbon-zero future.","PeriodicalId":35334,"journal":{"name":"Biochemist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44949720","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}
As we continue searching for the technologies that will halt global warming, let us take a moment to think about plants. A key contributor to our climate crisis is the accumulation of carbon dioxide in the atmosphere. Plants have been capturing carbon dioxide for billions of years, making them the most tried and tested carbon capture machinery on the planet. Plants fix carbon dioxide as part of photosynthesis. After years of research, we now know the key regulators of this process and have the knowledge to start engineering plants with increased photosynthetic capacity. In addition to improving the efficiency of carbon fixation, we must also find a way to stably store the carbon captured by plants. To achieve this, we can look to the below-ground part of the plant body – the root system. Plant roots are packed full of carbon and also exude carbon-rich molecules into the soil. Engineering future plants with deeper, more extensive root systems, with enhanced chemical composition that increases carbon content and reduces the rate of biodegradation, offers a way to store atmospheric carbon fixed by plants below ground for years to come. With optimized root systems, these plants would also be better equipped to explore their surrounding soils for water and nutrients, which would ultimately improve plant performance. This approach also offers a way to replenish our carbon-depleted soils, which would increase soil quality by improving water and nutrient retention. Harnessing the plants' natural ability to capture carbon, thus provides a way to not only restore balance to the carbon cycle, but also improve soil quality and future crop performance.
{"title":"The greenest revolution – harnessing the power of plants to help combat climate change","authors":"Wolfgang Busch, Charlotte Miller","doi":"10.1042/bio_2022_113","DOIUrl":"https://doi.org/10.1042/bio_2022_113","url":null,"abstract":"As we continue searching for the technologies that will halt global warming, let us take a moment to think about plants. A key contributor to our climate crisis is the accumulation of carbon dioxide in the atmosphere. Plants have been capturing carbon dioxide for billions of years, making them the most tried and tested carbon capture machinery on the planet. Plants fix carbon dioxide as part of photosynthesis. After years of research, we now know the key regulators of this process and have the knowledge to start engineering plants with increased photosynthetic capacity. In addition to improving the efficiency of carbon fixation, we must also find a way to stably store the carbon captured by plants. To achieve this, we can look to the below-ground part of the plant body – the root system. Plant roots are packed full of carbon and also exude carbon-rich molecules into the soil. Engineering future plants with deeper, more extensive root systems, with enhanced chemical composition that increases carbon content and reduces the rate of biodegradation, offers a way to store atmospheric carbon fixed by plants below ground for years to come. With optimized root systems, these plants would also be better equipped to explore their surrounding soils for water and nutrients, which would ultimately improve plant performance. This approach also offers a way to replenish our carbon-depleted soils, which would increase soil quality by improving water and nutrient retention. Harnessing the plants' natural ability to capture carbon, thus provides a way to not only restore balance to the carbon cycle, but also improve soil quality and future crop performance.","PeriodicalId":35334,"journal":{"name":"Biochemist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48468031","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}
Microbial communities are immensely important and occur nearly everywhere, but their inner workings are still being discovered. The early years of microbiome research have been dominated by cataloguing the sheer diversity of microbes in these communities. Now, more and more studies try to understand connections between the microbes, between the way communities are built and how they function, and between their activity and the effects on their surroundings, including host organisms like humans. Omics measurements, or meta-omics as they are called when multiple organisms are measured at the same time, are a cornerstone in this endeavour. Here, we will discuss why their integration is important, how it can be achieved, what pitfalls may be avoided and which approaches are taken by integrative studies.
{"title":"A beginner’s guide to integrating multi-omics data from microbial communities","authors":"A. Heintz‐Buschart, J. Westerhuis","doi":"10.1042/bio_2022_100","DOIUrl":"https://doi.org/10.1042/bio_2022_100","url":null,"abstract":"Microbial communities are immensely important and occur nearly everywhere, but their inner workings are still being discovered. The early years of microbiome research have been dominated by cataloguing the sheer diversity of microbes in these communities. Now, more and more studies try to understand connections between the microbes, between the way communities are built and how they function, and between their activity and the effects on their surroundings, including host organisms like humans. Omics measurements, or meta-omics as they are called when multiple organisms are measured at the same time, are a cornerstone in this endeavour. Here, we will discuss why their integration is important, how it can be achieved, what pitfalls may be avoided and which approaches are taken by integrative studies.","PeriodicalId":35334,"journal":{"name":"Biochemist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44400668","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}
Do you want to make your research more efficient and reliable? Have you wondered whether science could be environmentally sustainable and what you can do to help bring this about?
{"title":"Taking a LEAF out of the green lab book","authors":"C. Houghton, Saroj Saurya, Benjamin Foster","doi":"10.1042/bio_2022_110","DOIUrl":"https://doi.org/10.1042/bio_2022_110","url":null,"abstract":"Do you want to make your research more efficient and reliable? Have you wondered whether science could be environmentally sustainable and what you can do to help bring this about?","PeriodicalId":35334,"journal":{"name":"Biochemist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45993065","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}
Many aspects of doing a PhD feel like being thrown into the ocean without any help or support. This is especially the case when it comes to doing data analysis and coding. Unsurprisingly, as a PhD student you end up being inefficient with time and effort when it comes to doing your work. Sadly research culture currently doesn’t appreciate, fund or support these aspects of science as much as would be required to solve these problems. One of the first steps to changing this culture is through training and education of PhD students and early career researchers. Taking a course on being reproducible and open can lead you to being more productive and less stressed and, over time, teaching courses like these can help spread the awareness of these issues and slowly improve research culture.
{"title":"Escaping irreproducible research practices and spreading awareness through education and (re-)training","authors":"Bettina Lengger, Luke W. Johnston","doi":"10.1042/bio_2022_103","DOIUrl":"https://doi.org/10.1042/bio_2022_103","url":null,"abstract":"Many aspects of doing a PhD feel like being thrown into the ocean without any help or support. This is especially the case when it comes to doing data analysis and coding. Unsurprisingly, as a PhD student you end up being inefficient with time and effort when it comes to doing your work. Sadly research culture currently doesn’t appreciate, fund or support these aspects of science as much as would be required to solve these problems. One of the first steps to changing this culture is through training and education of PhD students and early career researchers. Taking a course on being reproducible and open can lead you to being more productive and less stressed and, over time, teaching courses like these can help spread the awareness of these issues and slowly improve research culture.","PeriodicalId":35334,"journal":{"name":"Biochemist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43275580","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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