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[前沿资讯 ] 天津工业生物技术研究所在技术驱动非粮原料生物制造微生物蛋白的前沿综述 进入全文
中国科学院天津工业生物技术研究所
中国科学院天津工业生物技术研究所吴信研究员团队从技术迭代的角度，全面梳理了微生物蛋白生物制造的变革，系统总结了利用液态（甲醇）、气态（CO2、甲烷）和固态（木质纤维素）等非粮原料规模化合成微生物蛋白的前沿技术突破，揭示了合成生物学与交叉技术创新如何重塑微生物蛋白生物制造系统。本团队前期的工作围绕甲醇作为一种可再生的C1化合物以及与二氧化碳氢化合成技术的重大突破，通过碳氮协同耦合代谢工程与基因组扰动等多重策略，有效提升天然甲基营养菌中甲醇向单细胞蛋白的定向转化效率，进而突破工业菌株性能极限，为利用甲醇作为碳源生物制造微生物蛋白大规模工业化生产提供了关键技术支持；在气态非粮生物制造微生物蛋白方面，通过构建大肠杆菌中的光-暗反应能量适配器，实现光驱动CO2同化的全细胞催化过程；通过电催化-生物耦合技术，可将电化学还原CO2生成的甲酸盐与微生物同化模块精准对接，为气态非粮原料的转化技术开辟了负碳生物制造微生物蛋白的新维度；在固态非粮原料生物合成微生物蛋白技术方面，该团队通过机器学习模型，基于木质纤维素结构特性破译出降解酶系组成的新算法，进而摆脱复杂性底物结构-多样性酶系构效关系的实验先验，精准定制了多种地源性木质纤维素来源的微生物蛋白，达到地源性农业废弃物资源利用与微生物蛋白生物合成“一草双收”效果。这些创新转化模式不仅提升了农业废弃物资源化利用经济价值，更开辟了农业废弃物规模化生物合成微生物蛋白的工业化新路径。
[科研项目 ] 美国匹兹堡大学“通过基于蛋白质纳米隔室的酶封装技术促进生物降解去除有机污染物”项目获美国国家科学基金会55万美元资助 进入全文
U.S. National Science Foundation
Many natural microorganisms, such as bacteria and fungi, can be used to degrade toxic pollutants and remediate contaminated sites. These microorganisms use a series of enzymes, called cascade enzymes, to break down pollutants step by step into less toxic end products. However, this process is slow and often allows toxic intermediates to accumulate. The goal of this CAREER project is to make biodegradation more efficient. The project will develop a new biotechnology, called protein nano-compartment (PNC)-based cargo encapsulation. Cascade enzymes will be encapsulated within PNCs, which will enable the enzymes to degrade pollutants and intermediates at similar rates. Toxic intermediates will not accumulate in the environment. The research will be integrated with education of students from middle schools and colleges. Successful completion of this project will create a more efficient, robust, and faster environmental remediation technology to protect human and environmental health. This CAREER project plans to apply PNC-based enzyme co-localization to accelerate biodegradation efficiency in removing organic water contaminants. The central hypothesis is that attaching enzymes with affinity tags of varying molecular properties will allow their tunable co-localization within PNCs, thereby enabling optimization and enhancement of the kinetics and stability of enzyme cascades for contaminant degradation. The study will integrate techniques in biodegradation, synthetic biology, and metabolic flux analysis to systematically characterize the effect of PNC co-localization on enzyme cascade efficiency. The proposed work will establish quantitative correlations between affinity tag properties and enzyme encapsulation efficiency. Building on these correlations, the study will explore how to strategically control the co-localization of biodegradative cascade enzymes within PNCs and analyze how this co-localization affects their kinetics in contaminant removal and stability against environmental factors under controlled in vitro conditions. Lastly, the PNC co-localization of biodegradative cascade enzymes will be assessed under cellular environments, and isotope-labeled metabolic flux analysis will be employed to develop a fundamental understanding of how the in vivo co-localization affects the rate, flux, and specificity of organic contaminant biodegradation in cells. The project includes an education plan aiming to 1) foster the education of college students in STEM and their participation in environmental engineering; 2) educate and train next-generation environmental engineers on the fundamentals, real-world applications, and opportunities of PNC encapsulation and biodegradation; and 3) promote public awareness and understanding of biodegradation as a sustainable solution for environmental protection and remediation. These educational activities will be integrated throughout to improve academic success and broaden participation of college students in research, stimulate STEM interest in 6-12 graders, train a future workforce on biodegradation through research projects, and build a biodegradation website for public education and outreach. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
[学术文献 ] Growth of the maternal intestine during reproduction 进入全文
Cell
The organs of many female animals are remodeled by reproduction. Using the mouse intestine, a striking and tractable model of organ resizing, we find that reproductive remodeling is anticipatory and distinct from diet- or microbiota-induced resizing. Reproductive remodeling involves partially irreversible elongation of the small intestine and fully reversible growth of its epithelial villi, associated with an expansion of isthmus progenitors and accelerated enterocyte migration. We identify induction of the SGLT3a transporter in a subset of enterocytes as an early reproductive hallmark. Electrophysiological and genetic interrogations indicate that SGLT3a does not sustain digestive functions or enterocyte health; rather, it detects protons and sodium to extrinsically support the expansion of adjacent Fgfbp1-positive isthmus progenitors, promoting villus growth. Our findings reveal unanticipated specificity to physiological organ remodeling. We suggest that organ- and state-specific growth programs could be leveraged to improve pregnancy outcomes or prevent maladaptive consequences of such growth.
[学术文献 ] Identification of Subfamily Specific Residues within Highly Active and Promiscuous Alcohol Dehydrogenases 进入全文
ACS Catalysis
Enzyme selection is an essential process in the biobased production of chemicals. It is essential to develop a method to extract yet unknown useful enzymes from protein databases. Enzymes that exhibit substrate promiscuity and high activity hold the potential to access unknown reactions and mediate known reactions with a higher performance. Herein, we propose and validate a principal component analysis (PCA)-based classification method, termed MUSASHI (MUltiple-Sequence Alignment-based protein Selection via clustering using HIgh-dimensional analysis), to identify subfamily-specific residues that are highly conserved among promiscuous alcohol dehydrogenase (ADH). Specifically, zinc-dependent ADH homologues retrieved from the protein database were classified into 9 groups, and according to PCA-based clustering, the activities of 18 ADHs, with representative enzymes from each group, were characterized. As a result, we identified two promiscuous ADH groups: Group 1 ADH, efficient with short-chain and aromatic aldehydes, and Group 3 ADH, efficient with aliphatic and aromatic ketones. Sequence feature analysis then revealed subfamily-specific residues, which are highly conserved only in promiscuous ADH Groups 1 and 3, with the potential to biosynthesize a wide spectrum of target compounds. Tatumella ptyseos ADH, identified from Group 1 of this study, showed higher isobutanol and 2-phenylethanol bioconversions than that of a conventional ADH (Ahr). These results indicate that the MUSASHI method for subfamily-specific residue identification can enable optimal enzyme selection from protein databases.
[学术文献 ] Enhancing the thermal stability and activity of the engineered self-sufficient P450SPα-SOX by switching the domains linker 进入全文
International Journal of Biological Macromolecules
This work reports on the engineering of the linker between P450 SPα (CYP152B1) and sarcosine oxidase (SOX), with the aim of enhancing the structural rigidity of the fusion protein (SPα-SOX) and study the effect on its stability and catalytic performance. Differential scanning calorimetry shows that the construct bearing the rigid linker (SPα-rigidSOX) results in a higher energy barrier to unfolding (765 kcal/mol) compared to the previous fusion system (SPα-flexible-SOX) (561 kcal/mol), as well as a Tonset above 50 °C. Furthermore, residual CO-binding after heat treatment was investigated for both the fusion systems, and a 5.7 °C increase of the T50 of SPα-rigid-SOX is shown. Interestingly, a stabilized P420 semifolded state of the SPα is also observed after SPα-rigid-SOX incubation at high temperature (40°). The two fusion systems were studied at high temperature for the turnover of lauric acid: SPα-rigid-SOX shows a 98 % conversion yield using 5 mM substrate compared to the 24 % conversion of SPαflexibleSOX when the catalysis is carried out at 40 °C. Finally, the activity of the two constructs was tested using styrene as a substrate, and three products of catalysis were observed: styrene oxide (85 %), phenylacetaldehyde (0–3 %) and 2-phenylpropenal (12–15 %). Interestingly, 2-phenylpropenal is observed for the first time and only for the fusion enzymes. Also in this case, SPα-rigid-SOX outperformed SPα-flexible-SOX with a 3-fold higher conversion yield. Overall, we demonstrate that the rigid linker improves the fusion enzyme thermal stability and catalytic performance, both at high temperature and in mild conditions, resulting also in the production of new molecules of biotechnological interest.
[学术文献 ] Discovery to Engineering of Mycotoxin Deoxynivalenol Degrading Enzymes Based on the Specialized Glyoxalase I 进入全文
Advanced Science
Deoxynivalenol (DON) is a mycotoxin that is omnipresent in food and feed. Therefore, this study has focused on discovery, molecular characterization, and engineering of DON degrading enzymes, based on a DON isomerizing enzyme (e.g., the specialized glyoxalase I from Gossypium raimondii (Gr-SPG)). A molecular phylogeny-based sequence and structure analysis elucidated the evolutionary trajectory of the DON degrading enzymes. Ancestral sequence reconstruction led to the generation of thermostable evolutionary intermediates of SPG (e.g., Anc216). Molecular modeling and consensus protein design allowed to understand the structure and function relationships and also identify the key conserved mutations that influence catalytic activity and thermostability. Ultimately, a highly active and thermostable SPG (e.g., a quintuple mutant of Anc216 (Anc216_M5)) was constructed from a newly discovered extant SPG enzyme (OR9). The Anc216_M5 exhibited a T5010 of 68 °C, which is 16.3 °C higher than that of the wild-type enzyme. Furthermore, the engineered enzyme showed 40% greater DON degrading activity than OR9, which is significantly higher than that of Gr-SPG. Therefore, it is assumed that Anc216_M5 is promising as a DON-detoxifying biocatalyst.
