PDF(Pubmed)
Abstract：
A comprehensive pangenomic approach was employed to analyze the genomes of 75 type II methylotrophs spanning various genera. Our investigation revealed 256 exact core gene families shared by all 75 organisms, emphasizing their crucial role in the survival and adaptability of these organisms. Additionally, we predicted the functionality of 12 hypothetical proteins. The analysis unveiled a diverse array of genes associated with key metabolic pathways, including methane, serine, glyoxylate, and ethylmalonyl-CoA (EMC) metabolic pathways. While all selected organisms possessed essential genes for the serine pathway, Methylooceanibacter marginalis lacked serine hydroxymethyltransferase (SHMT), and Methylobacterium variabile exhibited both isozymes of SHMT, suggesting its potential to utilize a broader range of carbon sources. Notably, Methylobrevis sp. displayed a unique serine-glyoxylate transaminase isozyme not found in other organisms. Only nine organisms featured anaplerotic enzymes (isocitrate lyase and malate synthase) for the glyoxylate pathway, with the rest following the EMC pathway. Methylovirgula sp. 4MZ18 stood out by acquiring genes from both glyoxylate and EMC pathways, and Methylocapsa sp. S129 featured an A-form malate synthase, unlike the G-form found in the remaining organisms. Our findings also revealed distinct phylogenetic relationships and clustering patterns among type II methylotrophs, leading to the proposal of a separate genus for Methylovirgula sp. 4M-Z18 and Methylocapsa sp. S129. This pangenomic study unveils remarkable metabolic diversity, unique gene characteristics, and distinct clustering patterns of type II methylotrophs, providing valuable insights for future carbon sequestration and biotechnological applications.
OBJECTIVE: Methylotrophs have played a significant role in methane-based product production for many years. However, a comprehensive investigation into the diverse genetic architectures across different genera of methylotrophs has been lacking. This study fills this knowledge gap by enhancing our understanding of core hypothetical proteins and unique enzymes involved in methane oxidation, serine, glyoxylate, and ethylmalonyl-CoA pathways. These findings provide a valuable reference for researchers working with other methylotrophic species. Furthermore, this study not only unveils distinctive gene characteristics and phylogenetic relationships but also suggests a reclassification for Methylovirgula sp. 4M-Z18 and Methylocapsa sp. S129 into separate genera due to their unique attributes within their respective genus. Leveraging the synergies among various methylotrophic organisms, the scientific community can potentially optimize metabolite production, increasing the yield of desired end products and overall productivity.
OBJECTIVE: Methylotrophs have played a significant role in methane-based product production for many years. However, a comprehensive investigation into the diverse genetic architectures across different genera of methylotrophs has been lacking. This study fills this knowledge gap by enhancing our understanding of core hypothetical proteins and unique enzymes involved in methane oxidation, serine, glyoxylate, and ethylmalonyl-CoA pathways. These findings provide a valuable reference for researchers working with other methylotrophic species. Furthermore, this study not only unveils distinctive gene characteristics and phylogenetic relationships but also suggests a reclassification for Methylovirgula sp. 4M-Z18 and Methylocapsa sp. S129 into separate genera due to their unique attributes within their respective genus. Leveraging the synergies among various methylotrophic organisms, the scientific community can potentially optimize metabolite production, increasing the yield of desired end products and overall productivity.
摘要：
采用全面的全基因组方法分析了75种跨越各个属的II型甲基营养菌的基因组。我们的调查揭示了所有75种生物共有256个确切的核心基因家族，强调它们在这些生物的生存和适应性中的关键作用。此外,我们预测了12种假设蛋白质的功能.该分析揭示了与关键代谢途径相关的各种基因，包括甲烷,丝氨酸,乙醛酸盐，和乙基丙二酰辅酶A（EMC）代谢途径。虽然所有选定的生物都拥有丝氨酸途径的必需基因，marginalis缺乏丝氨酸羟甲基转移酶（SHMT），和变异的甲基杆菌表现出两种SHMT同工酶，表明其利用更广泛碳源的潜力。值得注意的是,甲基brevissp.显示出在其他生物中未发现的独特的丝氨酸-乙醛酸转氨酶同工酶。只有9种生物具有乙醛酸途径的回补酶（异柠檬酸裂合酶和苹果酸合酶），其余的遵循EMC途径。甲基virgulasp.4MZ18通过从乙醛酸和EMC途径获得基因而脱颖而出，和Methylocapsasp。S129具有A型苹果酸合酶，与其余生物体中的G型不同。我们的发现还揭示了II型甲基营养动物之间不同的系统发育关系和聚类模式，导致提出了Methylovirgulasp。4M-Z18和Methylocapsasp。S129.这项全基因组研究揭示了显着的代谢多样性，独特的基因特征，和II型甲基营养菌的不同聚类模式，为未来的碳封存和生物技术应用提供有价值的见解。
目的：甲基化生物在基于甲烷的产品生产中发挥了重要作用。然而,缺乏对甲基营养菌不同属的不同遗传结构的全面调查。这项研究通过增强我们对甲烷氧化中涉及的核心假设蛋白质和独特酶的理解来填补这一知识空白。丝氨酸,乙醛酸盐，和乙基丙二酰辅酶A途径。这些发现为研究其他甲基营养物种的研究人员提供了有价值的参考。此外，这项研究不仅揭示了独特的基因特征和系统发育关系，而且还提出了对Methylovirgulasp的重新分类。4M-Z18和Methylocapsasp。S129由于其各自属内的独特属性而分为不同的属。利用各种甲基营养生物之间的协同作用，科学界可以潜在地优化代谢物的生产，提高所需最终产品的产量和整体生产率。
目的：甲基化生物在基于甲烷的产品生产中发挥了重要作用。然而,缺乏对甲基营养菌不同属的不同遗传结构的全面调查。这项研究通过增强我们对甲烷氧化中涉及的核心假设蛋白质和独特酶的理解来填补这一知识空白。丝氨酸,乙醛酸盐，和乙基丙二酰辅酶A途径。这些发现为研究其他甲基营养物种的研究人员提供了有价值的参考。此外，这项研究不仅揭示了独特的基因特征和系统发育关系，而且还提出了对Methylovirgulasp的重新分类。4M-Z18和Methylocapsasp。S129由于其各自属内的独特属性而分为不同的属。利用各种甲基营养生物之间的协同作用，科学界可以潜在地优化代谢物的生产，提高所需最终产品的产量和整体生产率。
