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Phage-mediated horizontal gene transfer and its implications for the human gut microbiome

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Gastroenterology Report 2022年第1期10卷 78-89页

作者： Tatiana Borodovich Andrey N.Shkoporov R.Paul Ross Colin Hill APC Microbiome Ireland University College CorkCorkIreland School of Microbiology University College CorkCorkIreland

horizontal gene transfer(HGT)in the microbiome has profound consequences for human health and *** spread of antibiotic resistance genes,virulence,and pathogenicity determinants predominantly occurs by way of *** exists of extensive horizontal transfer in the human gut *** transduction is a type of HGT event in which a bacteriophage transfers non-viral DNA from one bacterial host cell to *** abundance of tailed bacteriophages in the human gut suggests that transduction could act as a significant mode of HGT in the gut *** we review in detail the known mechanisms of phage-mediated HGT,namely specialized and generalized transduction,lateral transduction,gene-transfer agents,and molecular piracy,as well as methods used to detect phage-mediated HGT,and discuss its potential implications for the human gut microbiome.

关键词： gut phageome horizontal gene transfer gene transduction phage-mediated gene transfer

The statistical power of k-mer based aggregative statistics for alignment-free detection of horizontal gene transfer

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Synthetic and Systems Biotechnology 2019年第3期4卷 150-156页

作者： Guan-Da Huang Xue-Mei Liu Tian-Lai Huang Li-C.Xia School of Physics and Optoelectronics South China University of TechnologyGuangzhou510640China Department of Medicine Stanford University School of MedicineStanfordCA94305USA

Alignment-based database search and sequence comparison are commonly used to detect horizontal gene transfer(HGT).However,with the rapid increase of sequencing depth,hundreds of thousands of contigs are routinely assembled from metagenomics studies,which challenges alignment-based HGT analysis by overwhelming the known reference *** HGT by k-mer statistics thus becomes an attractive *** alignment-free statistics have been demonstrated in high performance and efficiency in wholegenome and transcriptome *** adapt k-mer statistics for HGT detection,we developed two aggregative statistics T^(S)_(sum ) and T^(*)_(sum),which subsample metagenome contigs by their representative regions,and summarize the regional D^(S) _(2) and D^(*)_(2)metrics by their upper *** systematically studied the aggregative statistics’power at different k-mer size using *** analysis showed that,in general,the power of T^(S)_(sum) and T^(*)_(sum) increases with sequencing coverage,and reaches a maximum power>80%at k=6,with 5%Type-I error and the coverage ratio>*** statistical power ofT^(S)_(sum) and T^(*)_(sum) was evaluated with realistic simulations of HGT mechanism,sequencing depth,read length,and base *** expect these statistics to be useful distance metrics for identifying HGT in metagenomic studies.

关键词： Alignment-free sequence comparison k-mer horizontal gene transfer Statistical power

Unexpected complex horizontal gene transfer in teleost fish

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Current Zoology 2023年第2期69卷 222-223页

作者： Zhiqiang Han Shengyong Xu Tianxiang Gao Fishery College Zhejiang Ocean UniversityZhoushanZhejiang 316002China

horizontal gene transfer(HGT)is a common occurrence across all domains of ***,most HGT events were reported between single-celled organisms or parasites and hosts(Van Etten and Bhattacharya 2020).A type II antifreeze protein(AFP)gene was the first and sole evidence of HGT direct vertebrate-to-vertebrate DNA *** is only found in 3 widely separated branches of teleost fishes(herring,sea raven,and smelts),sharing amino acid similarity up to 80%(Graham et al.2008).

关键词： horizontal gene transfer teleost fish

In silico Analysis of the Potential Infection Mechanisms of Magnaporthe grisea from horizontal gene transfer Hypothesis

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Genomics, Proteomics & Bioinformatics 2009年第3期7卷 77-86页

作者： Chunyang Li Ying Wang Hao Peng Hejiao Bian Mingwei Min Longfei Chen Qian Liu Jinku Bao School of Life Sciences Sichuan University Chengdu 610064 China China National Center for Biotechnology Development Beijing 100081 China

horizontal gene transfer （HGT） has long been considered as a principal force for an organism to gain novel genes in genome evolution. Homology search, phylogenetic analysis and nucleotide composition analysis are three major objective approaches to arguably determine the occurrence and directionality of HGT. Here, 21 genes that possess the potential to horizontal transfer were acquired from the whole genome of Magnaporthe grisea according to annotation, among which three candidate genes （corresponding protein accession numbers are EAA55123, EAA47200 and EAA52136） were selected for further analysis. According to BLAST homology results, we subsequently conducted phylogenetic analysis of the three candidate HGT genes. Moreover, nucleotide composition analysis was conducted to further validate these HGTs. In addition, the functions of the three candidate genes were searched in COG database. Consequently, we conclude that the gene encoding protein EAA55123 is transferred from Clostridium perfringens. Another HGT event is between EAA52136 and a certain metazoan＇s corresponding gene, but the direction remains uncertain. Yet, EAA47200 is not a transferred gene.

关键词： Magnaporthe grisea infection mechanism horizontal gene transfer homology phylogenetic analysis nucleotide composition

Strand-biased gene Distribution in Bacteria Is Related to both horizontal gene transfer and Strand-biased Nucleotide Composition

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Genomics, Proteomics & Bioinformatics 2012年第4期10卷 186-196页

作者： Hao Wu Hongzhu Qu Ning Wan Zhang Zhang Songnian Hu Jun Yu CAS Key Laboratory of Genome Sciences and Information Beifing Institute of GenomicsChinese Academy of SciencesBeijing 101300China

Although strand-biased gene distribution （SGD） was described some two decades ago, the underlying molecular mechanisms and their relationship remain elusive. Its facets include, but are not limited to, the degree of biases, the strand-preference of genes, and the influence of background nucleotide composition variations. Using a dataset composed of 364 non-redundant bacterial genomes, we sought to illus- trate our current understanding of SGD. First, when we divided the collection of bacterial genomes into non-polC and polC groups according to their possession of DnaE isoforms that correlate closely with taxonomy, the SGD of the polC group stood out more sig- nificantly than that of the non-polC group. Second, when examining horizontal gene transfer, coupled with gene functional conservation （essentiality） and expressivity （level of expression）, we realized that they all contributed to SGD. Third, we further demonstrated a weaker G-dominance on the leading strand of the non-polC group but strong purine dominance （both G and A） on the leading strand of the polC group. We propose that strand-biased nucleotide composition plays a decisive role for SGD since the polC-bearing genomes are not only AT-rich but also have pronounced purine-rich leading strands, and we believe that a special mutation spectrum that leads to a strong purine asymmetry and a strong strand-biased nucleotide composition coupled with functional selections for genes and their functions are both at work.

关键词： Strand-biased gene distribution Strand-biased nucleotide composition horizontal gene transfer Purine asymmetry GC content

VERTICAL HEREDITY VS. horizontal gene transfer: A CHALLENGE TO BACTERIAL CLASSIFICATION

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Journal of Systems Science & Complexity 2003年第3期16卷 307-314页

作者： HAO Bailin(Institute of Theoretical Physics, Academy of Chinese Sciences, Beijing 100080, China Senior International Fellow of the Santa Fe Institute T-Life Research Center, Fudan University,Shanghai 200433, China)QI Ji(Institute of Theoretical Physics, Beijing 100080, China) Institute of Theoretical Physics Academy of Chinese Sciences 北京 100080 Institute of Theoretical Physics Chinese Academy of Sciences 北京 100080

The diversity and classification of microbes has been a long-standing *** phylogeny of the prokaryotes based on comparison of the 16S rRNA sequences of the small ribosomal subunit has led to a reasonable tree of life in the late 1970s. How-ever, the availability of more and more complete bacterial genomes has brought about complications instead of refinement of the tree. In particular, it turns out that different choice of genes may tell different history. This might be caused by possible horizontal gene transfer (HGT) among species. There is an urgent need to develop phylogenetic methods that make use of whole genome data. We describe a new approach in molecular phylogeny,namely, tree construction based on K-tuple frequency analysis of the genomic *** aside the technicalities, we emphasize the transition from randomness to determin-ism when the string length K increases and try to comment on the challenge mentioned in the title.

关键词： prokaryote phylogeny horizontal gene transfer fitness compositionaldistance

Characterizing proteases in an Antarctic Janthinobacterium sp. isolate: Evidence of a protease horizontal gene transfer event

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Advances in Polar Science 2015年第1期26卷 88-95页

作者： Cecilia Martinez-Rosales Juan José Marizcurrena Andrés Iriarte Natalia Fullana Héctor Musto Susana Castro-Sowinski Sección Bioquímica y Biología Molecular Facultad de Ciencias Universidad de la República (Udela R) Igua 4225 11400 Montevideo Uruguay Microbiología Molecular Instituto de Investigaciones Biológicas Clemente Estable (IIBCE).Av Italia 3318 11600Montevideo Uruguay Dpto de Bioquímica y Genómica Microbiana and Dpto de Genómica (IIBCE) Dpto de Desarrollo Biotecnológico Instituto de Higiene Facultad de Medicina Udela R Laboratorio de Organización y Evolución del Genoma Facultad de Ciencias Udela R

We report the isolation of a cold-adapted bacterium belonging to the genus Janthinobacterium （named AU 11）, from a water sample collected in Lake Uruguay （King George Island, South Shetlands）. AUI 1 （growth between 4℃ and 30℃） produces a single cold-active extracellular protease （ExPAU11）, differentially expressed at low temperature. ExPAU11 was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry （MALDI-ToF MS） as an alkaline metallo-protease （70% coverage with an extracellular protease of Janthinobacterium sp. PI12）, and by protease-inhibitor screening identified as a serine-protease. To the best of our knowledge this is the first experimental evidence of a cold-active extracellular protease produced by Janthinobacterium. Furthermore, we identified a serine-protease gene （named JSP8A） showing 60% identity （98% query coverage） to subtilisin peptidases belonging to the $8 family （S8A subfamily） of many cyanobacteria. A phylogenetic analysis of the JSP8A protease, along with related bacterial protein sequences, confirms that JSP8A clusters with S8A subtilisin sequences from different cyanobacteria, and is clearly separated from SSA bacterial sequences of other phyla （including its own）. An analysis of the genomic organization around JSP8A suggests that this protease gene was acquired in an event that duplicated a racemase gene involved in transforming L- to D-amino acids. Our results suggest that AU11 probably acquired this subtilisin-like protease gene by horizontal gene transfer （HGT） from a cyanobacterittrn. We discuss the relevance of a bacterial protease-HGT in the Antarctic environment in light of this hypothesis.

关键词： Antarctic cold-active protease horizontal gene transfer Janthinobacterium subtilisin

A Novel Mycoreovirus from Sclerotinia sclerotiorum Reveals Cross-family horizontal gene transfer and Evolution of Diverse Viral Lineages

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A Novel Mycoreovirus from Sclerotinia sclerotiorum Reveals C...

New genes acquired from plants by horizontal gene transfer may have contributed to adaptive divergence in Valsa spp.

中国植物病理学会2016年学术年会

作者： LIU Li-jiang GAO Li-xia CHENG Jia-sen FU Yan-ping LIU Hui-quan JIANG Dao-hong XIE Jia-tao State Key Laboratory of Agricultural Microbiology The Provincial Key Lab of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural University Key Laboratory of Biology and genetic Improvement of Oil Crops Ministry of Agriculture of People's Republic of ChinaOil Crops Research InstituteChinese Academy of Agricultural Sciences NWAFU-PU Joint Research Center State Key Laboratory of Crop Stress Biology for Arid AreasCollege of Plant ProtectionNorthwest A&F University

As the largest dsRNA virus family,the evolutionary relationship of reoviruses remains still unclear for the lack of enough representative members and evolutionary ***,we performed the molecular cloning and complete genome of a novel mycoreovirus Sclerotinia sclerotiorum Reovirus 1(SsReV1) which had a genome of 28 055 base pairs(bp) and 11 dsRNA *** combination with unique molecular features,virions shape and composition,and phylogenetic analysis,SsReV1 was distinct from all known reoviruses and may represent a new taxonomic unit in the Reoviridae *** importantly,two conserved domains,double-stranded RNA binding motif(dsRBM,pfam 00035) and reovirus sigma C capsid protein(ReoC,pfam04582),were identified in the genome of SsReV1,that were widespread in diverse virus lineages in the further *** comparison and phylogenetic analysis revealed that multiple cross-family horizontal gene transfer(HGT) events may occur among reoviruses,dsDNA viruses,single-stranded RNA viruses and even cellular ***,the dsRBM of SsReV1 shared a closest phylogenetic relationship with those of two human proteins(Q7Z6F6/P19525,E7EVJ4) with a strong *** results indicate that SsReV1 is a new taxonomic representative in the Reoviridae family and reoviruses may have a large-scale gene-communications with other virus lineages more common than previously recognized,providing new insights into the diversity,global ecology and evolution of reoviruses and segmented dsRNA viruses.

关键词： Sclerotinia sclerotiorum Mycoreovirus horizontal gene transfer

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New genes acquired from plants by horizontal gene transfer m...