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Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

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science China life sciences 2025年第1期 232-248页

作者： Yaohan Jiang Xiao Chen Chundi Wang Liping Lyu Saleh A.Al-Farraj Naomi A.Stover Feng Gao Key Laboratory of evolution & marine biodiversity (Ministry of Education) and institute of evolution & marine biodiversity Ocean University of China marine college Shandong University Zoology Department College of ScienceKing Saud University Department of Biology Bradley University Laboratory for marine Biology and Biotechnology Qingdao Marine Science and Technology Center

Sexual reproduction first appeared in unicellular protists and has continued to be an essential biological process in almost all *** protists, which contain both germline and somatic genomes within a single cell, have evolved a special form of sexual reproduction called conjugation that involves mitosis, meiosis, fertilization, nuclear differentiation, genome rearrangement, and the development of unique cellular structures. The molecular basis and mechanisms of conjugation vary dramatically among ciliates, and many details of the process and its regulation are still largely unknown. In order to better comprehend these processes and mechanisms from an evolutionary perspective, this study provides the first comprehensive overview of the transcriptome and proteome profiles during the entire life cycle of the newly-established marine model ciliate Euplotes vannus. Transcriptome analyses from 14 life cycle stages(three vegetative stages and 11 sexual stages) revealed over 26,000 genes that are specifically expressed at different stages, many of which are related to DNA replication,transcription, translation, mitosis, meiosis, nuclear differentiation, and/or genome rearrangement. Quantitative proteomic analyses identified 338 proteins with homologs associated with conjugation and/or somatic nuclear development in other ciliates, including dicer-like proteins, Hsp90 proteins, RNA polymerase Ⅱ and transcription elongation factors, ribosomal-associated proteins, and ubiquitin-related proteins. Four of these homologs belong to the PIWI family, each with different expression patterns identified and confirmed by RT-qPCR,which may function in small RNA-mediated genome rearrangement. Proteins involved in the nonhomologous end-joining pathway are induced early during meiosis and accumulate in the developing new somatic nucleus, where more than 80% of the germline sequences are eliminated from the somatic genome. A number of new candidate genes and proteins likely t

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Functional characterization of an orexin neuropeptide in amphioxus reveals an ancient origin of orexin/orexin receptor system in chordate

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science China(life sciences) 2019年第12期62卷 1655-1669页

作者： Peng Wang Meng Wang Liping Zhang Shenjie Zhong Wanyue Jiang Ziyue Wang Chen Sun Shicui Zhang Zhenhui Liu institute of evolution & marine biodiversity College of Marine Life Science Ocean University of China

Amphioxus belongs to the subphylum cephalochordata, an extant representative of the most basal chordates, whose regulation of endocrine system remains ambiguous. Here we clearly demonstrated the existence of a functional orexin neuropeptide in amphioxus, which is able to interact with orexin receptor, activate both PKC and PKA pathways, decrease leptin expression, and stimulate lipogenesis. We also showed the transcription level of amphioxus orexin was affected by fasting or temperature,indicating a role of this gene in the regulation of energy balance. In addition, the expression of the amphioxus orexin was detected at cerebral vesicle, which has been proposed to be a homolog of the vertebrate brain. These data collectively suggest that a functional orexin neuropeptide has already emerged in amphioxus, which provide insights into the evolutionary origin of orexin in chordate and the functional homology between the cerebral vesicle and vertebrate brain.

关键词： amphioxus orexin neuropeptide evolution

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Presence of a long nuclear-localization signal sequence in homeodomain transcription factor Nkx 1.2

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Journal of Oceanology and Limnology 2024年第2期42卷 620-626页

作者： Xinyi LI Lihui CHEN Xinyuan WANG Chen SUN Guangdong JI Guobin HU Zhenhui LIU college of marine life science and institute of evolution&marine biodiversity Ocean University of ChinaQingdao 266003China Laoshan Laboratory Qingdao 266237China

Homeodomains,a 60-amino acid sequence encoded by 180 nucleotides,are highly conserved DNA-binding motifs that are present in a variety of transcription factors in species ranging from yeast to *** NKX proteins belong to the homeodomain(HD)-containing transcription factor *** play vital roles in the regulation of ***1-2 is one member of the NKX *** present,information about its nuclear localization signal(NLS)sequence is *** studied the NLS sequence of zebrafish Nkx1.2 by introducing sequence changes such as deletion,mutation,and truncation,and identified an NLS motif(QNRRTKWKKQ)that is localized at the C-terminus of the ***,the deletion of two amino acid residues(RR)in this NLS motif prevents Nkx1.2 from entering the nucleus,indicating that the two amino acids are essential for Nkx1.2 nuclear ***,the NLS motif alone is unable to target cytoplasmic protein glutathione S-transferase(GST)to the *** intact homeodomain is necessary for mediating the complete nuclear transport of cytoplasmic *** most nuclear import proteins with short NLS sequences,a long NLS is present in zebrafish *** also demonstrated that the sequences of homeodomain of NKX1.2 are well conserved among different *** study is informative to verify the function of the NKX1.2 protein.

关键词： NKX1.2 NKX protein homeodomain nuclear localization signal(NLS) nuclear transport

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RpL38 modulates germ cell differentiation by controlling Bam expression in Drosophila testis

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science China(life sciences) 2024年第11期67卷 2411-2425页

作者： Yang Fang Fengchao Zhang Fangzhen Zhao Jiajia Wang Xinkai Cheng Fei Ye Jiayu He Long Zhao Ying Su Key Laboratory of evolution&marine biodiversity(Ministry of Education)and institute of evolution&marine biodiversity Ocean University of ChinaQingdao 266003China college of marine life sciences Ocean University of ChinaQingdao 266003China Fisheries college Ocean University of ChinaQingdao 266003China

Switching from mitotic spermatogonia to meiotic spermatocytes is critical to producing haploid sperms during male germ cell ***,the underlying mechanisms of this switch remain largely *** Drosophila melanogaster,the gene RpL38 encodes the ribosomal protein L38,one component of the 60S subunit of *** found that its depletion in spermatogonia severely diminished the production of mature sperms and thus led to the infertility of male *** examining the germ cell differentiation in testes,we found that RpL38-knockdown blocked the transition from spermatogonia to spermatocytes and accumulated spermatogonia in the *** understand the intrinsic reason for this blockage,we conducted proteomic analysis for these spermatogonia *** from the control spermatogonia,the accumulated spermatogonia in RpL38-knockdown testes already expressed many spermatocyte markers but lacked many meiosis-related proteins,suggesting that spermatogonia need to prepare some important proteins for meiosis to complete their switch into ***,we found that the expression of bag of marbles(bam),a crucial determinant in the transition from spermatogonia to spermatocytes,was inhibited at both the mRNA and protein levels upon RpL38 *** also confirmed that the bam loss phenocopied RpL38 RNAi in the testis phenotype and transcriptomic ***,overexpressing bam was able to fully rescue the testis abnormality and infertility of RpL38-knockdown flies,indicating that bam is the key effector downstream of RpL38 to regulate spermatogonia ***,our data suggested that germ cells start to prepare meiosis-related proteins as early as the spermatogonial stage,and RpL38 in spermatogonia is required to regulate their transition toward spermatocytes in a bamdependent manner,providing new knowledge for our understanding of the transition process from spermatogonia to spermatocytes in Drosophila

关键词： Drosophila melanogaster spermatogenesis RpL38 spermatogonia bam

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The Mechanisms and Applications of Quorum Sensing(QS) and Quorum Quenching(QQ)

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Journal of Ocean University of China 2019年第6期18卷 1427-1442页

作者： ZHANG Jingjing FENG Tao WANG Jiayi WANG Yan ZHANG Xiao-Hua college of marine life sciences Ocean University of ChinaQingdao 266003China Laboratory for marine Ecology and Environmental science Qingdao National Laboratory for Marine Science and TechnologyQingdao 266071China institute of evolution&marine biodiversity Ocean University of ChinaQingdao 266003China

Quorum sensing(QS)is a regulatory system that regulates the behavior of microbial populations by sensing the concentration of signal molecules that are spontaneously produced and released by *** strategy of blocking the QS system and inhibiting the production of virulence factors is termed as quorum quenching(QQ).This strategy attenuates virulence without killing the pathogens,thereby weakening the selective pressure on pathogens and postponing the evolution of QQ-mediated drug *** recent years,there have been significant theoretical and practical developments in the field of QS and *** particular,with the development and utilization of marine resources,more and more marine microbial species have been found to be regulated by these two mechanisms,further promoting the research progress of QS and *** this review,we described the diversity of QS signals and QS-related regulatory systems,and then introduced mechanisms related to QS interference,with particular emphasis on the description of natural QQ enzymes and chemicals acting as QS ***,the exploitation of quorum sensing quenchers and the practical application of QQ were introduced,while some QQ strategies were proposed as promising tools in different fields such as medicine,aquaculture,agriculture and biological pollution prevention areas.

关键词： quorum sensing quorum quenching marine microorganisms antibiotic resistance

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Long-term in-vitro culture and subculture of the hemocytes of swimming crab Portunus trituberculatus

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Journal of Oceanology and Limnology 2023年第5期41卷 1918-1939页

作者： Liwen GUO Yaqi ZHAO Huarong GUO Key Laboratory of marine Genetics and Breeding Ministry of EducationCollege of Marine Life SciencesOcean University of ChinaQingdao 266003China institute of evolution&marine biodiversity Ocean University of ChinaQingdao 266003China

Crab cell line,especially continuous crab cell line,can provide us a useful tool for studies on the virology,immunology,and molecular biology of ***,no continuous crab cell line has been available due to the lacking of suitable medium and the occurrence of *** this study,long-term in vitro culture conditions for both two-(2D)and three-dimensions(3D)were successfully developed for the circulating hemocytes of swimming crab Portunus trituberculatus,designated as PTH *** 2D culture,a novel crab basic medium in osmolarity of 990–1100 mOsm/kg was optimized for the first time,which is different from Leibovitz's L-15 medium in mainly the components of amino acids,containing double strengths of the contents of free amino acid mixture in the crab *** an optimal crab growth medium was developed by supplementing 5%fetal bovine serum,50-g/L yeast extract powder,20-μg/L basic fibroblast growth factor and epidermal growth factor into the optimal crab basic medium,and found that it could support a long-term survival of PTH cells in a healthy monolayer up to 347 days and partially break through the mitosis-arrest of crab cells evidenced by the obvious increase of proliferating potential detected in the 10-d primarily cultured PTH *** 2D cultured PTH cells could be successfully sub-cultured for 11 times by physical flushing method and well cryopreserved in liquid *** 3D culture,using the same crab growth medium,the PTH cell aggregates could be easily formed and healthily maintained on the surface of solidified Matrigel or in the ultra-low-attachment plate with a survival rate of 50%–60%on Day *** work largely improved the primary culture and subculture of crab cells and will facilitate the establishment of continuous crab cell line.

关键词： crab Portunus trituberculatus hemocyte long-term cell culture subculture 3D culture

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From germline genome to highly fragmented somatic genome:genome-wide DNA rearrangement during the sexual process in ciliated protists

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marine life science & Technology 2024年第1期6卷 31-49页

作者： Liping Lyu Xue Zhang Yunyi Gao Tengteng Zhang Jinyu Fu Naomi A.Stover Feng Gao Key Laboratory of evolution&marine biodiversity(Ministry of Education) and Institute of Evolution&Marine BiodiversityOcean University of ChinaQingdao 266003China Department of Biology Bradley UniversityPeoriaIL 61625USA Laoshan Laboratory Qingdao 266237China

Genomes are incredibly dynamic within diverse eukaryotes and programmed genome rearrangements(PGR)play important roles in generating genomic ***,genomes and chromosomes in metazoans are usually large in size which prevents our understanding of the origin and evolution of *** expand our knowledge of genomic diversity and the evolutionary origin of complex genome rearrangements,we focus on ciliated protists(ciliates).Ciliates are single-celled eukaryotes with highly fragmented somatic chromosomes and massively scrambled germline *** in ciliates occurs extensively by removing massive amounts of repetitive and selfish DNA elements found in the silent germline genome dur-ing development of the somatic *** report the partial germline genomes of two spirotrich ciliate species,namely Strombidium *** and Halteria grandinella,along with the most compact and highly fragmented somatic genome for *** provide the first insights into the genome rearrangements of these two species and compare these features with those of other *** analyses reveal:(1)DNA sequence loss through evolution and during PGR in *** has combined to produce the most compact and efficient nanochromosomes observed to date;(2)the compact,transcriptome-like somatic genome in both species results from extensive removal of a relatively large number of shorter germline-specific DNA sequences;(3)long chromosome breakage site motifs are duplicated and retained in the somatic genome,revealing a complex model of chromosome fragmentation in spirotrichs;(4)gene scrambling and alternative pro-cessing are found throughout the core spirotrichs,offering unique opportunities to increase genetic diversity and regulation in this group.

关键词： Alternative processing Ciliates Gene scrambling Genome rearrangement Germline genome Somatic genome

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Phylogenomic analyses shed light on the relationships of chiton superfamilies and shell‑eye evolution

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marine life science & Technology 2023年第4期5卷 525-537页

作者： Xu Liu Julia D.Sigwart Jin Sun Key Laboratory of evolution&marine biodiversity(Ministry of Education)and institute of evolution&marine biodiversity Ocean University of ChinaQingdao 266003China Laoshan Laboratory Qingdao 266237China Department of marine Zoology Senckenberg Research Institute and Natural History Museum Frankfurt60325 Frankfurt Am MainGermany

Mollusca is the second-largest animal phylum with over 100,000 extant species representing eight *** 1000 extant species in the class Polyplacophora,chitons have a relatively constrained morphology but with some notable *** genera possess“shell eyes”,i.e.,true eyes with a lens and retina that are embedded within the dorsal *** phylogeny of the major chiton clades is mostly well established,in a set of superfamily-level and higher level taxa supported by various approaches,including morphological studies,multiple gene markers,mitogenome-phylogeny,and phylotranscriptomic ***,one critical lineage has remained unclear,namely Schizochiton which was controversially suggested as being the potential independent origin of chiton shell ***,with the draft genome sequencing of Schizochiton incisus(superfamily Schizochitonoidea)plus assemblies of transcriptome data from other polyplacophorans,we present phylogenetic reconstructions using both mitochondrial genomes and phylogenomic approaches with multiple *** found that phylogenetic trees from mitogenomic data are inconsistent,reﬂecting larger scale confounding factors in molluscan ***,a consistent and robust topology was generated with protein-coding genes using diﬀerent models and *** results support Schizochitonoidea as the sister group to other Chitonoidea in Chitonina,in agreement with the established classiﬁ*** with evidence from fossils,our phylogenetic results suggest that the earliest origin of shell eyes is in Schizochitonoidea,and that these structures were also gained secondarily in other genera in *** results have generated a holistic review of the internal relationship within Polyplacophora,and a better understanding of the evolution of Polyplacophora.

关键词： Chiton Mollusca Phylogenomics Polyplacophora Shell eyes

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Transcriptome analysis reveals immune-related genes in tissues of Vibrio anguillarum-infected turbot Scophthalmus maximus

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Journal of Oceanology and Limnology 2024年第1期42卷 332-344页

作者： Yuting SONG Maqsood Ahmed SOOMRO Xianzhi DONG Guobin HU college of marine life sciences Ocean University of ChinaQingdao 266003China institute of evolution&marine biodiversity Ocean University of ChinaQingdao 266003China institute of Biophysis Chinese Academy of SciencesBeijing 100101China

Turbot Scophthalmus maximus is an important mariculture fish species with high economic ***,the bacterial diseases caused by Vibrio anguillarum infection bring huge economic losses to the turbot aquaculture *** understand the immune response of the turbot against *** infection and to explore novel immune-related genes,the transcriptome analysis of turbot spleen and gills were conducted after *** *** expressed genes(DEGs)were identified in spleen and gill of the turbot amounted to 17261 and 16436,respectively.A large number of immunerelated DEGs were enriched in cytokine-cytokine receptor interaction signaling pathway,and the others by the kyoto encyclopedia of genes and genomes(KEGG)*** gene ontology(GO)classification analysis revealed that *** infection had the greatest effect on biological processes and cellular *** immune-related DEGs were identified in the spleen(cstl.1,egfl6,lamb21,v2rx4,calcr,and gpr78a)and gills(ghra,sh3gl2a,cst12,inhbaa,cxcl8,and il-1b)by heat *** proteinprotein interaction(PPI)networks were constructed to analyze the immune *** results demonstrate that the maturation and antigen processing of major histocompatibility complex(MHC)class II molecule,and calcitonin-or adrenomedullin-regulated physiological activity were important events in the immunity of turbot against *** *** the gills,the protein interactions in TGF-βsignaling pathway,production of inflammatory factors,and endocytosis regulation were most *** research laid a foundation for discovering novel immune-related genes and enriching the knowledge of immune mechanisms of turbot against *** infection.

关键词： Scophthalmus maximus Vibrio anguillarum transcriptome differentially expressed genes immune mechanism

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Effect of temperature and photoperiod on maturation of Cephalothrix hongkongiensis(Nemertea: Palaeonemertea)

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Chinese Journal of Oceanology and Limnology 2014年第4期32卷 764-772页

作者：李应东宋肖跃张珊珊朱林孙世春 institute of evolution and marine biodiversity Ocean University of China

The limited knowledge about the relationships between environmental factors and the maturation and reproductive seasonality of nemerteans is mostly obtained from field studies, and in many cases is conjectural. Few species have been studied under well-controlled laboratory conditions. In this work, the effects of temperature and photoperiod on gonad development and spawning of Cephalothrix hongkongiensis were observed by rearing worms under different temperatures and photoperiods. Worms reared at 4~C and 6~C showed no growth or gonadal development, and all died within 109 days. At 8~C and 12~C, gonads could be seen from 90 days to the termination of the 360-day experiment, but no spawning was observed. Worms maintained at 16, 24, and 28~C showed both gonadal development and spawning, and matured faster at higher temperatures. Under a fixed temperature （16℃）, photoperiod did not have any significant impact on maturation and spawning. It is likely that temperature plays a major role in regulating the maturation and reproductive cycle of C. hongkongiensis.

关键词： temperature photoperiod gonad development reproduction Cephalothrix hongkongiensis Nemertea

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