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Occurrence of human pathogenic bacteria carrying antibiotic resistance genes revealed by metagenomic approach: A case study from an aquatic environment

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Journal of Environmental Sciences 2019年第6期31卷 248-256页

作者： Renjun Zhou Shenzheng Zeng Dongwei Hou Jian Liu Shaoping Weng Jianguo He Zhijian Huang state key laboratory of biocontrol Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering School of MarineSciences Sun Yat-sen University School of Life Sciences Sun Yat-sen University

Antibiotic resistance genes(ARGs), human pathogenic bacteria(HPB), and HPB carrying ARGs are public issues that pose a high risk to aquatic environments and public health. Their diversity and abundance in water, intestine, and sediments of shrimp culture pond were investigated using metagenomic approach. A total of 19 classes of ARGs, 52 HPB species, and 7 species of HPB carrying ARGs were found. Additionally, 157, 104, and 86 subtypes of ARGs were detected in shrimp intestine, pond water, and sediment samples, respectively. In all the samples, multidrug resistance genes were the highest abundant class of ARGs. The dominant HPB was Enterococcus faecalis in shrimp intestine, Vibrio parahaemolyticus in sediments, and Mycobacterium yongonense in water, respectively. Moreover, E. faecalis(contig Intestine_364647)and Enterococcus faecium(contig Intestine_80272) carrying efr A, efr B and ANT(6)-Ia were found in shrimp intestine, Desulfosaricina cetonica(contig Sediment_825143) and Escherichia coli(contig Sediment_188430) carrying mex B and APH(3′)-IIa were found in sediments, and Laribacter hongkongensis(contig Water_478168 and Water_369477), Shigella sonnei(contig Water_880246),and Acinetobacter baumannii(contig Water_525520) carrying sul1, sul2, ere A, qac H, OXA-21, and mph D were found in pond water. Mobile genetic elements(MGEs) analysis indicated that horizontal gene transfer(HGT) of integrons, insertion sequences, and plasmids existed in shrimp intestine, sediment, and water samples, and the abundance of integrons was higher than that of other two MGEs. The results suggested that HPB carrying ARGs potentially existed in aquatic environments, and that these contributed to the environment and public health risk evaluation.

关键词： Antibiotic resistance genes Human pathogenic bacteria Mobile genetic elements Aquatic environment

Computational RNomics:Structure identification and functional prediction of non-coding RNAs in silico

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Science China(Life Sciences) 2010年第5期53卷 548-562页

作者： ZHENG LingLing & QU LiangHu key laboratory of Gene Engineering of the Ministry of Education,state key laboratory for biocontrol,Sun Yat-sen University,Guangzhou 510275,China 1. key laboratory of Gene Engineering of the Ministry of Education State Key Laboratory for Biocontrol Sun Yat-sen University Guangzhou 510275 China

The eukaryotic genome contains varying numbers of non-coding RNA(ncRNA) genes."Computational RNomics" takes a multidisciplinary approach,like information science,to resolve the structure and function of ***,we review the main issues in "Computational RNomics" of data storage and management,ncRNA gene identification and characterization,ncRNA target identification and functional prediction,and we summarize the main methods and current content of "computational RNomics".

关键词： non-coding RNA eukaryote computational RNomics

Soil nitrogen availability intensifies negative density-dependent effects in a subtropical forest

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Journal of Plant Ecology 2020年第3期13卷 281-287页

作者： Fengmin Huang Minxia Liang Yi Zheng Xubing Liu Yuxin Chen Wenbin Li Shan Luo Shixiao Yu Department of Ecology School of Life Sciences/State Key Laboratory of BiocontrolSun Yat-sen UniversityGuangzhouChina

Aims The importance of density-dependent mortality in maintaining tree species diversity is widely ***,density-dependent effects may vary in magnitude and direction with different abiotic conditions in *** predictions surmise that density-dependent effects may vary with soil available nitrogen(AN),but this still needs to be *** We analyzed the density-dependent effects on survival of newly germinated seedlings for 18 common species based on a long-term seedling census across environmental gradients in a subtropical *** also conducted a root lesion detection experiment for five species to investigate the potential effects of pathogens on variation in density-dependent disease between rich and poor AN *** Findings The seedling dynamics analysis revealed that the strength of density-dependent effects increased with AN,shifting from neutral or positive with low AN to negative with high *** of the five tree species had stronger density-dependent effects on root lesions in rich AN environments than in poor AN environments,which is consistent with the results of a long-term seedling dynamics *** also found higher species diversity in rich AN environments,which may be promoted by the stronger negative density-dependent *** the seedling dynamic analysis and root lesion detection experiment revealed stronger negative density-dependent effects in higher AN environment,resulting from stronger disease pressure by soil *** study emphasized the importance of considering context dependence when testing the density dependence hypotheses.

关键词： density dependence root lesions soil available nitrogen soil pathogen subtropical forest

A novel RNA-guided RNA-targeting CRISPR tool

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Science China(Life Sciences) 2016年第8期59卷 854-856页

作者： Dandan Zhang Zhenxiang Li Bingyu Yan Jian-Feng Li key laboratory of Gene Engineering of the Ministry of Education State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources School of Life Sciences Sun Yat-sen University

Clustered regularly interspaced short palindromic repeats （CRISPR）/CRISPR-associated protein （Cas） technology has emerged as a programmable RNA-guided DNA-targeting tool for sequence-specific genome editing in diverse organ- isms. The most frequently used CRISPR/Cas system, which is based on the bacterium Streptococcus pyogenes Cas9 （SpCas9） endonuclease, has been repurposed into a suite of versatile tools for numerous DNA-manipulating activities beyond genome editing （Jiang and Marraffini, 2015）. How- ever, progress in converting the CRISPR/SpCas9 system into a sequence-specific RNA-manipulating platform has been limited. A recent study published in Science by Abudayyeh and colleagues （Abudayyeh et al., 2016） has identified Leptotrichia shahii C2c2 （LshC2c2） to be a novel programmable RNA-targeting endoribonuclease with great potential to reshape the landscape of future RNA research.

关键词： targeting RNA guided programmable editing diverse regularly repeats DNA visualization

DNA-guided genome editing tool

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Science China(Life Sciences) 2016年第7期59卷 740-741页

作者： Dandan Zhang Jian-Feng Li key laboratory of Gene Engineering of the Ministry of Education State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources School of Life Sciences Sun Yat-sen University

Technologies for targeted modification of eukaryotic genomes are of great value for elucidating and manipulating gene functions in fundamental and applied biological *** the past two decades,genome editing tools have evolved quickly from random DNA mutagenesis-inducing chemicals or ionizing radiation to programmable sequencespecific nucleases(SSNs)with the CRISPR/Cas technology as the most significant breakthrough(Gaj et al.,2013).

关键词：编辑工具基因组 DNA 引导序列特异性搜索技术基本操作改性过程

New insight into the role of miRNAs in leukemia

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Science China(Life Sciences) 2009年第3期52卷 224-231页

作者： ZHANG Hua & CHEN YueQin key laboratory of Genetic Engineering of the Ministry of Education,state key laboratory of biocontrol,Sun Yan-Sen University,Guangzhou 510275,China 1. key laboratory of Genetic Engineering of the Ministry of Education State Key Laboratory of Biocontrol Sun Yan-Sen University Guangzhou 510275 China

Recent studies have shown that microRNAs(miRNAs) play an important role in cell differentiation,growth,and death,including the functional study of miRNAs in *** date,miRNA expression profiles in many types of cancers have been identified and miRNA expression signatures associated with types and cytogenetics of leukemia have also been *** evidence has shown that miRNAs could function as either tumor suppressors or oncogenes in cancers such as leukemia,while other miRNAs might be benefitcial for diagnosis and prognosis,predicted to be newly developed *** this review,we summarize the recent progress about miRNAs in leukemia and present a miRNA-mediated network involved in differentiation,proliferation and apoptosis predicted to be the roles of miRNAs in the pathogenesis of leukemia.

关键词： miRNA leukemia regulation network clinical implication

Igniting autophagy through the regulation of phase separation

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Signal Transduction and Targeted Therapy 2020年第1期5卷 1911-1912页

作者： Shouheng Jin Jun Cui MOE key laboratory of Gene Function and Regulation State Key Laboratory of BiocontrolSchool of Life SciencesSun Yat-sen University510275 GuangzhouGuangdongChina

A recent paper published in Nature by Fujioka et *** that the Atg1(also known as ULK1 in mammals)complex undergoes phase separation to form a liquid-like biomolecular condensate,thereby promoting the formation of a preautophagosomal structure(PAS)to activate autophagy in yeast.1 This research discovered the details of a mechanism of phase separation underlying autophagy initiation and provided a better understanding of the biological condensates.

关键词： separation phase details

tRNAs as regulators in gene expression

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Science China(Life Sciences) 2009年第3期52卷 245-252页

作者： LI Yan & ZHOU Hui key laboratory of Gene Engineering of the Ministry of Education,state key laboratory for biocontrol,Sun Yan-Sen University Guangzhou 510275,China 1. key laboratory of Gene Engineering of the Ministry of Education State Key Laboratory for Biocontrol Sun Yan-Sen University Guangzhou 510275 China

Transfer RNAs(tRNAs) hold a central place in protein synthesis by interpreting the genetic information stored in DNA into the amino acid sequence of protein,thus functioning as "adaptor" *** recent years,however,various studies have shown that tRNAs have additional functions beyond participating in protein *** suffering from certain nutritional stresses,tRNAs change the level of aminoacylation to became uncharged,and these uncharged tRNAs act as effector molecules to regulate global gene expression,so that the stressed organism copes with the adverse environmental *** budding yeast and certain mammalian cells,the retrograde movement of mature tRNAs from cytoplasm to nucleus serves as a mechanism for the surveillance system within the nucleus to continue monitoring the integrity of *** the other hand,this retrograde action effectively reduces the global protein synthesis level under conditions of nutritional *** recently,various publications have shown that tRNAs are not stable molecules in an absolute *** certain physiological or environmental stresses,they are specifically cleaved into fragments of different lengths in the anticodon loop or anticodon left *** cleavages are not a meaningless random degradation ***,a novel class of signal molecules such as tRNA halves or sitRNAs may be produced,which are closely correlated with the modulation of global gene *** of the regulatory functions of tRNAs is a frontier,which seeks to reveal the structural and functional diversity of tRNAs as well as their vital functions during the expression of genetic information.

关键词： tRNA sitRNA gene expression regulation stress response

Type-ll Metacaspases Mediate the processing of Plant Elicitor Peptides in Arabidopsis

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Molecular Plant 2019年第11期12卷 1524-1533页

作者： Wenzhong Shen Jiuer Liu Jian-Feng Li state key laboratory of biocontrol Guangdong Provincial Key Laboratory of Plant ResourcesMOE Key Laboratory of Gene Function and RegulationSchool of Life SciencesSun Yat-sen UniversityGuangzhou 510275China

Plants can produce animal cytokine-like immune peptides,among which plant elicitor peptides(Peps)derive from the C termini of their precursors(PROPEPs).Recently,the functions of Peps have been expanded beyond plant ***,a long-standing enigma is how PROPEPs are processed into ***,we report that the Ca2+-dependent type-ll metacaspases(MCs)constitute the proteolytic enzymes to mediate PROPEP processing in *** protoplasts,co-expression of PROPEP1 with type-ll MCs,including MC4 to MC9,can promote the generation of processed *** of the catalytic cysteine residue in MC4 or the conserved arginine residue preceding the Pep1 sequence blocks PROPEP1 cleavage,whereas the bacterial elicitor flg22 enhances the MC4-mediated PROPEP1 ***4 cleaves PROPEP1 in vitro and also cleaves PROPEP2 to PROPEP8,but,surprisingly,not PROPEP6 in *** swapping between PROPEP1 and PROPEP6 suggests a hidden role of the sequence context upstream of the Pep sequence for PROPEP ***22-induced PROPEP1 processing and B otrytis cinerea resistance are severely impaired in the m c4/5/6/7 quadruple-mutant *** together,our study identifies the type-ll MCs as new players in Pep signaling,and lays the foundation for understanding the regulation of multifaceted functions of Peps in plant immunity and beyond.

关键词： immunity plant elicitor peptides proteolysis metacaspases Arabidopsis