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Development of MEMS directed evolution strategy for multiplied throughput and convergent evolution of cytochrome P450 enzymes

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Science China(Life Sciences) 2022年第3期65卷 550-560页

作者： Li Ma Fengwei Li Xingwang Zhang Hui Chen Qian Huang Jing Su Xiaohui Liu Tianjian Sun Bo Fang Kun Liu Dandan Tang Dalei Wu Wei Zhang Lei Du Shengying Li State Key Laboratory of Microbial Technology Shandong UniversityQingdao 266237China Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and TechnologyQingdao 266237China Shandong Provincial Key Laboratory of Synthetic Biology Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao 266101China College of Life Sciences Yantai UniversityYantai 264005China State Key Laboratory of Biobased Material and Green Papermaking Qilu University of Technology(Shandong Academy of Sciences)Jinan 250353China

Directed evolution(DE)inspired by natural evolution(NE)has been achieving tremendous successes in protein/enzyme ***,the conventional"one-protein-for-one-task"DE cannot match the"multi-proteins-for-multi-tasks"NE in terms of screening throughput and efficiency,thus often failing to meet the fast-growing demands for biocatalysts with desired *** this study,we design a novel"multi-enzymes-for-multi-substrates"(MEMS)DE model and establish the proof-ofconcept by running a NE-mimicking and higher-throughput screening on the basis of"two-P450 s-against-seven-substrates"(2P×7S)in one *** the multiplied throughput and improved hit rate,we witness a series of convergent evolution events of the two archetypal cytochrome P450 enzymes(P450 BM3 and P450 cam)in *** is anticipated that the new strategy of MEMS DE will find broader application for a larger repertoire of enzymes in the ***,structural and substrate docking analysis of the two functionally convergent P450 variants provide important insights into how distinct P450 active-sites can reach a common catalytic goal.

关键词： MEMS directed evolution cytochrome P450 enzymes high-throughput screening convergent evolution ambroxide 3β-hydroxylase

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convergent evolution inspired serrated structure for improving efficiency of soil imprinting and its mechanism investigation

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International Journal of Agricultural and Biological Engineering 2019年第4期12卷 16-26页

作者： Zhihong Zhang Ying Li Jin Tong Stephen Carr College of Agriculture and Food Kunming University of Science and TechnologyKunming 650500China United States Department of Agriculture Agricultural Research Service1680 Madison Ave.WoosterOhio 44691USA The Key Laboratory of Bionic Engineering Jilin UniversityChangchun 130025China International Soil and Water Renewables LLCSalemIndiana 47167USA

Remarkable geometrical similarities are found in digging claws of soil burrowing animals,in spite of the fact that they evolved *** on convergent evolution theory,this study innovatively proposed a bionic engineering perspective that focuses on general and analogous geometrical characteristics of soil *** was observed that soil animals with powerful burrowing ability have analogous serrated structures on their digging *** soil imprinting toothed wheel as the research object,the hypothesis that special serrated structures have the potential of reducing penetrating resistance from soil and enhancing digging efficiency for soil engaging component was *** convergent evolution inspired bionic serrated structures were utilized for the design of cutting edge on toothed ***,a toothed wheel that mounted with the conventional tooth and a bionic tooth were manufactured and tested in the soil *** showed that special bionic serrated structure could reduce the required draft force for toothed wheel;meanwhile increase the depth and volume of prepared *** was found that the soil-penetrating mechanism of the bionic toothed wheel behaved as saw cutting that similar to the digging behavior of soil burrowing *** of serrated structure has the ability to maximum stress concentrations in soil,thus increased the tendency of soil material to *** results indicate that the convergent evolution inspired bionic approach is novel and advantageous for the design of new soil engaging implements for working quality optimization and forward resistance reduction.

关键词： convergent evolution bionic serrated structure soil imprinting soil-engaging component bionic agricultural machinery

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Diet drives convergent evolution of gut microbiomes in bamboo-eating species

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Science China(Life Sciences) 2021年第1期64卷 88-95页

作者： Guangping Huang Xiao Wang Yibo Hu Qi Wu Yonggang Nie Jiuhong Dong Yun Ding Li Yan Fuwen Wei CAS Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing100101China University of Chinese Academy of Sciences Beijing100049China Beijing Milu Ecological Research Center Beijing100076China Center for Excellence in Animal evolution and Genetics Chinese Academy of SciencesKunming650223China State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing100101China

Gut microbiota plays a critical role in host physiology and *** coevolution between the host and its gut microbes facilitates animal adaptation to its specific ecological *** factors such as host diet and phylogeny modulate the structure and function of gut ***,the relative contribution of each factor in shaping the structure of gut microbiota remains *** giant(Ailuropoda melanoleuca)and red(Ailurus styani)pandas belong to different families of order *** have evolved as obligate bamboo-feeders and can be used as a model system for studying the gut microbiome convergent ***,we compare the structure and function of gut microbiota of the two pandas with their carnivorous relatives using 16S rRNA and metagenome *** found that both panda species share more similarities in their gut microbiota structure with each other than each species shares with its carnivorous *** indicates that the specialized herbivorous diet rather than host phylogeny is the dominant driver of gut microbiome convergence within *** analysis revealed that the symbiotic gut microbiota of both pandas possesses a high level of starch and sucrose metabolism and vitamin B12 *** findings suggest a diet-driven convergence of gut microbiomes and provide new insight into host-microbiota coevolution of these endangered species.

关键词： gut microbiome metagenome convergent evolution starch and sucrose metabolism vitamin B12 giant panda red panda

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Reaction mechanism of azoreductases suggests convergent evolution with quinone oxidoreductases

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Protein & Cell 2010年第8期1卷 780-790页

作者： Ali Ryan Chan-Ju Wang Nicola Laurieri Isaac Westwood Edith Sim Department of Pharmacology University of OxfordMansfield RoadOxfordOX13QTUK

Azoreductases are involved in the bioremediation by bacteria of azo dyes found in waste *** the gut flora,they activate azo pro-drugs,which are used for treatment of inflammatory bowel disease,releasing the active component 5-aminosalycilic *** bacterium *** has three azoreductase genes,paAzoR1,paAzoR2 and paAzoR3,which as recombinant enzymes have been shown to have different substrate *** mechanism of azoreduction relies upon tautomerisation of the substrate to the hydrazone *** report here the characterization of the *** azoreductase enzymes,including determining their thermostability,cofactor preference and kinetic constants against a range of their favoured *** expression levels of these enzymes during growth of *** are altered by the presence of azo *** is shown that enzymes that were originally described as azoreductases,are likely to act as NADH quinone *** low sequence identities observed among NAD(P)H quinone oxidoreductase and azoreductase enzymes suggests convergent evolution.

关键词： azoreductase enzyme mechanism NAD(P)H quinone oxidoreductase enzyme characterisation convergent evolution

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convergent evolution of genome size of mangrove

Convergent evolution of genome size of mangrove

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中国植物学会第十六次全国会员代表大会暨85周年学术年会

作者： Shao Shao Shaohua Xu Suhua Shi State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources Sun Yat-sen University

Mangroves are woody plants growing in the extreme environment of intertidal zone on tropical and subtropical *** invading intertidal zone,mangroves have convergently evolved similar phenotypic traits and the underlying genic convergence（Xu et al.2017）.Since the high salinity of the intertidal zone may directly affect the cellular environment,mangroves also extensively modified their amino acid compositions and reduced gene family *** genome-wide changes indicate that mangroves may have unique genome features such as genome *** this study,we collected and measured the genome sizes of 21 true mangroves from independent clades,and 8 mangrove *** with non-mangrove,mangroves have significantly downsized genomes（P ＜10-9）,whereas mangrove associates do not show this difference（P = 0.26）.Comparisons based on phylogenetic relationships show that the genome size reduction occurred independently in the true mangrove *** the reduction in genome size has evolved independently at least 7 times,it appears to be an adaptive strategy of these woody plants to live in the intertidal *** the environment of intertidal zone are with high salinity and low nutrient availability,the small genome size may increase genome stability and reduce energy consuming.

关键词： convergent evolution adaptation extreme environment genome reduction mangroves

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A comparison of MHC classⅡDRB sequences in crocodiles:Trans-species or convergent evolution?

A comparison of MHC classⅡDRB sequences in crocodiles:Trans...

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第七届全国野生动物生态与资源保护学术研讨会

作者： LI En1,WU Xiaobing~1,Wu Hailong~1,YAN Peng~1,WANG Chaolin~2,WANG Renping~2 1 Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Science,Anhui Normal University,241000 Wuhu,China 2 Anhui Research Center of Chinese Alligator Reproduction,Xuancheng 242034,China

Allelic diversity at major histocompatibility complex(MHC)genes is thought to be maintained by balancing selection over long periods of time,even across multiple speciation ***-species sharing of MHC alleles among species has been documented in mammals, fishes and birds,but in crocodiles,the results are *** we investigated the genetic variation at MHC classⅡDRB locus in Nile crocodile(Crocodylus niloticus)and compare with 16 previously published orthologous sequences and three other crocodile *** allelic variability was observed among sequences within each of these species,indicating extensive MHC *** substitution rates(dN)exceeded synonymous substitution rates (dS)greatly within the antigen-binding sites(ABS),suggesting the maintenance of polymorphism by balancing *** analysis of these sequences clearly supports the hypothesis of trans-species evolution.A comparison of sequence patterns also revealed the trans-species allele sharing of the DRB gene in crocodiles,which suggested that some variation could have been generated through gene conversion events.

关键词： MHC Crocodilia trans-species evolution convergent evolution

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Comparative transcriptomic evidence of physiological changes and potential relationships in vertebrates under different dormancy states

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Zoological Research 2024年第2期45卷 341-354页

作者： Yu-Han Niu Li-Hong Guan Cheng Wang Hai-Feng Jiang Guo-Gang Li Lian-Dong Yang Shun-Ping He State Key Laboratory of Freshwater Ecology and Biotechnology Institute of HydrobiologyChinese Academy of SciencesWuhanHubei 430072China College of Life Sciences Qinghai Normal UniversityXiningQinghai 810008China Academy of Plateau Science and Sustainability Qinghai Normal UniversityXiningQinghai 810016China Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province Qinghai Normal UniversityXiningQinghai 810008China College of Life Sciences and Technology Xinxiang Medical UniversityXinxiangHenan 453003China College of Animal Science and Technology Northwest A&F UniversityYanglingShaanxi 712100China

Dormancy represents a fascinating adaptive strategy for organisms to survive in unforgiving *** a period of dormancy,organisms often exhibit exceptional *** period is typically divided into hibernation and aestivation based on seasonal ***,the mechanisms by which organisms adapt to their environments during dormancy,as well as the potential relationships between different states of dormancy,deserve further ***,we selected Perccottus glenii and Protopterus annectens as the primary subjects to study hibernation and aestivation,*** on histological and transcriptomic analysis of multiple organs,we discovered that dormancy involved a coordinated functional response across *** analyses revealed noteworthy disparities between the two dormant species in their responses to extreme ***,similarities in gene expression patterns pertaining to energy metabolism,neural activity,and biosynthesis were noted during hibernation,suggesting a potential correlation between hibernation and *** further explore the relationship between these two phenomena,we analyzed other dormancy-capable species using data from publicly available *** comparative analysis revealed that most orthologous genes involved in metabolism,cell proliferation,and neural function exhibited consistent expression patterns during dormancy,indicating that the observed similarity between hibernation and aestivation may be attributable to convergent *** conclusion,this study enhances our comprehension of the dormancy phenomenon and offers new insights into the molecular mechanisms underpinning vertebrate dormancy.

关键词： Hibernation Aestivation Multi-organs convergent evolution

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A chromosome-level genome of electric catfish(Malapterurus electricus)provided new insights into order Siluriformes evolution

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Marine Life Science & Technology 2024年第1期6卷 1-14页

作者： Meiru Liu Yue Song Suyu Zhang Lili Yu Zengbao Yuan Hengjia Yang Mengqi Zhang Zhuocheng Zhou Inge Seim Shanshan Liu Guangyi Fan Huanming Yang College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China BGI-Qingdao BGI-ShenzhenQingdao 266555China BGI-Shenzhen Shenzhen 518083China Professional Committee of Native Aquatic Organisms and Water Ecosystem of China Fisheries Association Beijing 100125China Integrative Biology Laboratory College of Life SciencesNanjing Normal UniversityNanjing 210023China State Key Laboratory of Agricultural Genomics BGI-ShenzhenShenzhen 518083China

The electric catfish(Malapterurus electricus),belonging to the family Malapteruridae,order Siluriformes(Actinopterygii:Ostariophysi),is one of the six branches that has independently evolved electrical *** assembled a 796.75 Mb *** genome and anchored 88.72%sequences into 28 *** family analysis revealed 295 expanded gene families that were enriched on functions related to glutamate *** evolutionary analyses of electric organs among different lineage of electric fishes further revealed that the coding gene of rho guanine nucleotide exchange factor 4-like(arhgef4),which is associated with G-protein coupled receptor(GPCR)signaling pathway,underwent adaptive parallel *** identification suggests visual degradation in catfishes,and an important role for taste in environmental *** findings fill in the genomic data for a branch of electric fish and provide a relevant genetic basis for the adaptive evolution of Siluriformes.

关键词： Electric fish Karyotype analysis convergent evolution Environmental adaptation Historical effective population size

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Hologenomic insights into mammalian adaptations to myrmecophagy

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National Science Review 2023年第4期10卷 24-36页

作者： Shao-Chen Cheng Chun-Bing Liu Xue-Qin Yao Jing-Yang Hu Ting-Ting Yin Burton K.Lim Wu Chen Guo-Dong Wang Cheng-Lin Zhang David M.Irwin Zhi-Gang Zhang Ya-Ping Zhang Li Yu State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan School of Life SciencesYunnan University State Key Laboratory of Genetic Resources and evolution Kunming Institute of ZoologyChinese Academy of Sciences Department of Natural History Royal Ontario Museum Guangzhou Zoo Center for Excellence in Animal evolution and Genetics Kunming Institute of ZoologyChinese Academy of Sciences Beijing Zoo Department of Laboratory Medicine and Pathobiology University of Toronto

Highly specialized myrmecophagy(ant-and termite-eating) has independently evolved multiple times in species of various mammalian orders and represents a textbook example of phenotypic evolutionary convergence. We explored the mechanisms involved in this unique dietary adaptation and convergence through multi-omic analyses, including analyses of host genomes and transcriptomes, as well as gut metagenomes, in combination with validating assays of key enzymes’ activities, in the species of three mammalian orders(anteaters, echidnas and pangolins of the orders Xenarthra, Monotremata and Pholidota, respectively) and their relatives. We demonstrate the complex and diverse interactions between hosts and their symbiotic microbiota that have provided adaptive solutions for nutritional and detoxification challenges associated with high levels of protein and lipid metabolisms, trehalose degradation, and toxic substance detoxification. Interestingly, we also reveal their spatially complementary cooperation involved in degradation of ants’ and termites’ chitin exoskeletons. This study contributes new insights into the dietary evolution of mammals and the mechanisms involved in the coordination of physiological functions by animal hosts and their gut commensals.

关键词： myrmecophagy adaptive evolution hologenome genomics metagenomics convergent evolution

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Lack of evolutionary convergence in multiple primary lung cancer suggests insufficient specificity of personalized therapy

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Journal of Genetics and Genomics 2023年第5期50卷 330-340页

作者： Hua Cheng Ziyan Guo Xiaoyu Zhang Xiao-Jin Wang Zizhang Li Wen-Wen Huo Hong-Cheng Zhong Xiao-Jian Li Xiang-Wen Wu Wen-Hao Li Zhuo-Wen Chen Tian-Chi Wu Xiang-Feng Gan Bei-Long Zhong Vassily ALyubetsky Leonid Yu Rusin Junnan Yang Qiyi Zhao Qing-Dong Cao Jian-Rong Yang Department of Thoracic Surgery The Fifth Affiliated HospitalSun Yat-Sen UniversityZhuhaiGuangdong 519000China Department of Genetics and Biomedical Informatics Zhongshan School of MedicineSun Yat-sen UniversityGuangzhouGuangdong 510080China Program in Cancer Research Zhongshan School of MedicineThe Fifth Affiliated HospitalSun Yat-sen UniversityGuangzhouGuangdong 510080China Kharkevich Institute for Information Transmission Problems Russian Academy Sciences Moscow 127051Russia Department of Mathematical Logic and Theory of Algorithms Faculty of Mechanics and MathematicsLomonosov Moscow State UniversityMoscow 119991Russia Department of Infectious Diseases Third Affiliated HospitalSun Yat-Sen UniversityGuangzhouGuangdong 510630China Guangdong Provincial Key Laboratory of Liver Disease Research the Third Affiliated Hospital Sun Yat-sen UniversityGuangzhouGuangdong 510630China Key Laboratory of Tropical Disease Control Ministry of EducationSun Yat-sen UniversityGuangzhouGuangdong 510080China

Multiple primary lung cancer(MPLC)is an increasingly prevalent subtype of lung *** to recent genomic studies,the different lesions of a single MPLC patient exhibit functional similarities that may reflect evolutionary *** perform whole-exome sequencing for a unique cohort of MPLC patients with multiple samples from each lesion *** our own and other relevant public data,evolutionary tree reconstruction reveals that cancer driver gene mutations occurred at the early trunk,indicating evolutionary contingency rather than adaptive ***,tumors from the same MPLC patient are as genetically diverse as those from different patients,while within-tumor genetic heterogeneity is significantly ***,the aberrant molecular functions enriched in mutated genes for a sample show a strong overlap with other samples from the same tumor,but not with samples from other tumors or other ***,there is no evidence of adaptive convergence during the evolution of *** importantly,the similar between-tumor diversity and between-patient diversity suggest that personalized therapies may not adequately account for the genetic diversity among different tumors in an MPLC *** fully exploit the strategic value of precision medicine,targeted therapies should be designed and delivered on a per-lesion basis.

关键词： Multiple primary lung cancer Cancer evolution convergent evolution

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