刘树林
比较细菌基因组学
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- 姓名:刘树林
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学术头衔:
博士生导师
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学科领域:
医学微生物学
- 研究兴趣:比较细菌基因组学
刘树林,微生物学教授,现任北京大学医学部病原生物学系主任。1982年毕业于哈尔滨医科大学,学士;1985年,北京医科大学,硕士;1990年,日本岐阜大学,博士。自1990年起,在加拿大卡尔加里大学从事细菌基因组研究工作。2002年2月回国工作。主要研究领域是比较细菌基因组学。
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20
【期刊论文】Genome Plasticity and ori-ter Rebalancing in Salmonella typhi
刘树林, Gui-Rong Liu, *?? Wei-Qiao Liu, § Randal N. Johnston, || Kenneth E. Sanderson, § Shao-Xian Li, ? and Shu-Lin Liu*??
,-0001,():
-1年11月30日
Genome plasticity resulting from frequent rearrangement of the bacterial genome is a fascinating but poorly understood phenomenon. First reported in Salmonella typhi, it has been observed only in a small number of Salmonella serovars, although the over 2,500 known Salmonella serovars are all very closely related. To gain insights into this phenomenon and elucidate its roles in bacterial evolution, especially those involved in the formation of particular pathogens, we systematically analyzed the genomes of 127 wild-type S. typhi strains isolated from many places of the world and compared them with the two sequenced strains, Ty2 and CT18, attempting to find possible associations between genome rearrangement and other significant genomic features. Like other host-adapted Salmonella serovars, S. typhi contained large genome insertions, including the 134 kb Salmonella pathogenicity island, SPI7. Our analyses showed that SPI7 disrupted the physical balance of the bacterial genome between the replication origin (ori) and terminus (ter) when this DNA segment was inserted into the genome, and rearrangement in individual strains further changed the genome balance status, with a general tendency toward a better balanced genome structure. In a given S. typhi strain, genome diversification occurred and resulted in different structures among cells in the culture. Under a stressed condition, bacterial cells with better balanced genome structures were selected to greatly increase in proportion; in such cases, bacteria with better balanced genomes formed larger colonies and grew with shorter generation times. Our results support the hypothesis that genome plasticity as a result of frequent rearrangement provides the opportunity for the bacterial genome to adopt a better balanced structure and thus eventually stabilizes the genome during evolution.
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刘树林, Kai-Yu Wu, Gui-Rong Liu, , Wei-Qiao Liu, Austin Q. Wang, Sen Zhan, Kenneth E. Sanderson, Randal N. Johnston, and Shu-Lin Liu, *
JOURNAL OF BACTERIOLOGY, July 2005, p.4720-4727,-0001,():
-1年11月30日
Salmonella enterica serovar Gallinarum is a fowl-adapted pathogen, causing typhoid fever in chickens. It has the same antigenic formula (1,9,12:-:-) as S. enterica serovar Pullorum, which is also adapted to fowl but causes pullorum disease (diarrhea). The close relatedness but distinct pathogeneses make this pair of fowl pathogens good models for studies of bacterial genomic evolution and the way these organisms acquired pathogenicity. To locate and characterize the genomic differences between serovar Gallinarum and other salmonellae, we constructed a physical map of serovar Gallinarum strain SARB21 by using I-CeuI, XbaI, and AvrII with pulsed-field gel electrophoresis techniques. In the 4,740-kb genome, we located two insertions and six deletions relative to the genome of S. enterica serovar Typhimurium LT2, which we used as a reference Salmonella genome. Four of the genomic regions with reduced lengths corresponded to the four prophages in the genome of serovar Typhimurium LT2, and the others contained several smaller deletions relative to serovar Typhimurium LT2, including regions containing srfJ, std, and stj and gene clusters encoding a type I restriction system in serovar Typhimurium LT2. The map also revealed some rare rearrangements, including two inversions and several translocations. Further characterization of these insertions, deletions, and rearrangements will provide new insights into the molecular basis for the specific host-pathogen interactions and mechanisms of genomic evolution to create a new pathogen.
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【期刊论文】Diversity of Genome Structure in Salmonella enterica Serovar Typhi Populations?
刘树林, Sushma Kothapalli, Satheesh Nair, Suneetha Alokam, Tikki Pang, Rasik Khakhria, ? David Woodward, Wendy Johnson, Bruce A. D. Stocker, § Kenneth E. Sanderson, * and Shu-Lin Liu,
JOURNAL OF BACTERIOLOGY, Apr. 2005, p.2638-2650,-0001,():
-1年11月30日
The genomes of most strains of Salmonella and Escherichia coli are highly conserved. In contrast, all 136 wild-type strains of Salmonella enterica serovar Typhi analyzed by partial digestion with I-CeuI (an endonuclease which cuts within the rrn operons) and pulsed-field gel electrophoresis and by PCR have rearrangements due to homologous recombination between the rrn operons leading to inversions and translocations. Recombination between rrn operons in culture is known to be equally frequent in S. enterica serovar Typhi and S. enterica serovar Typhimurium; thus, the recombinants in S. enterica serovar Typhi, but not those in S. enterica serovar Typhimurium, are able to survive in nature. However, even in S. enterica serovar Typhi the need for genome balance and the need for gene dosage impose limits on rearrangements. Of 100 strains of genome types 1 to 6, 72 were only 25.5 kb off genome balance (the relative lengths of the replichores during bidirectional replication from oriC to the termination of replication [Ter]), while 28 strains were less balanced (41 kb off balance), indicating that the survival of the best-balanced strains was greater. In addition, the need for appropriate gene dosage apparently selected against rearrangements which moved genes from their accustomed distance from oriC. Although rearrangements involving the seven rrn operons are very common in S. enterica serovar Typhi, other duplicated regions, such as the 25 IS200 elements, are very rarely involved in rearrangements. Large deletions and insertions in the genome are uncommon, except for deletions of Salmonella pathogenicity island 7 (usually 134 kb) from fragment I-CeuI-G and 40-kb insertions, possibly a prophage, in fragment I-CeuI-E. The phage types were determined, and the origins of the phage types appeared to be independent of the origins of the genome types.
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【期刊论文】Comparative Genomics viaWavelet Analysis for Closely Related Bacteria
刘树林, Jiuzhou Song, TonyWare, Shu-Lin Liu, M. Surette
EURASIP Journal on Applied Signal Processing 2004: 1, 5-12,-0001,():
-1年11月30日
Comparative genomics has been a valuable method for extracting and extrapolating genome information among closely related bacteria. The efficiency of the traditional methods is extremely influenced by the software method used. To overcome the problem here, we propose using wavelet analysis to perform comparative genomics. First, global comparison using wavelet analysis gives the difference at a quantitative level. Then local comparison using keto-excess or purine-excess plots shows precise positions of inversions, translocations, and horizontally transferred DNA fragments.We firstly found that the level of energy spectra difference is related to the similarity of bacteria strains; it could be a quantitative index to describe the similarities of genomes. The strategy is described in detail by comparisons of closely related strains: S.typhi CT18, S.typhi Ty2, S.typhimurium LT2, H.pylori 26695, and H.pylori J99.
comparative genomics,, gene discovery,, wavelet analysis,, bacterial genome
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【期刊论文】Phylogenetic clusters of rhizobia revealed by genome structures
刘树林, ZHENG Junfang, LIU Guirong, , ZHU Wanfu, ZHOU Yuguang & LIU Shulin
Science in China Ser. C Life Sciences 2004 Vol.47 No.3 268-278,-0001,():
-1年11月30日
Rhizobia, bacteria that fix atmospheric nitrogen, are important agricultural resources. In order to establish the evolutionary relationships among rhizobia isolated from different geographic regions and different plant hosts for systematic studies, we evaluated the use of physical structure of the rhizobial genomes as a phylogenetic marker to categorize these bacteria. In this work, we analyzed the features of genome structures of 64 rhizobial strains. These rhizobial strains were divided into 21 phylogenetic clusters according to the features of genome structures evaluated by the endonuclease I-CeuI. These clusters were supported by 16S rRNA comparisons and genomic sequences of four rhizobial strains, but they are largely different from those based on the current taxonomic scheme (except 16S rRNA).
rhizobia,, phylogeny,, genome structure
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刘树林, 郑君芳①, 刘桂荣①②, 朱万孚①, 周宇光③, 刘树林①②**
中国科学,2003,33(6):514~524,-0001,():
-1年11月30日
阐明根瘤菌之间的系统发育关系,可使人们更有效地利用这些自然资源,因而对农业生产和环境保护具有重大意义。通过-Ceu 酶切表明64株根瘤菌的基因组结构特征,揭示根瘤菌的系统发育关系。结果表明,64株根瘤菌依据基因组结构特征可聚为21个系统发育群,这些群与16SrRNA分子聚群结果大致相符,但与现行的根瘤菌分类体系所得结果有较大差异。
根瘤菌, 系统发育, 基因组结构
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刘树林, 衣美英, 刘桂荣, 朱永红, 朱万孚
中国华微生物学和免疫学杂志,2003,23(12):941~945,-0001,():
-1年11月30日
目的通过基因组结构分析对临床分离的Eseherichia coil(E.coli)进行分型, 并探讨分型与临床疾病的关系。方法取临床不同疾病病人的痰、尿、血、分泌物等标本,分离E.coil。用I-Ceu I酶切全基因组DNA,用脉冲场凝胶电泳分离DNA片段后,根据酶切图谱的异同进行分型。结果从临床上分离的64株E.coli中,62株有7个I-Ceu I酶切位点,2株有8个I-Ceu I酶切位点。菌株间I-Ceu I酶切图谱差异明显。这些菌株根据基因组结构的差异分为32个型,分型与疾病之间的对应关系分散。结论临床分离的E.coli基因组结构存在多样性,其与临床疾病之间的关系有待进一步探讨。
I-Ceu I, E., coli, 基因组结构, 基因组分型
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【期刊论文】Wavelet to predict bacterial ori and ter: a tendency towards a physical balance
刘树林, Jiuzhou Song, Antony Ware and Shu-Lin Liu*,
,-0001,():
-1年11月30日
Background: Chromosomal DNA replication in bacteria starts at the origin (ori) and the two replicores propagate in opposite directions up to the terminus (ter) region. We hypothesize that the two replicores need to reach ter at the same time to maintain a physical balance; DNA insertion would disrupt such a balance, requiring chromosomal rearrangements to restore the balance. To test this hypothesis, we needed to demonstrate that ori and ter are in a physical balance in bacterial chromosomes. Using wavelet analysis, we documented GC skew, AT skew, purine excess and keto excess on the published bacterial genomic sequences to locate the turning (minimum and maximum) points on the curves. Previously, the minimum point had been supposed to correlate with ori and the maximum to correlate with ter. Results: We observed a strong tendency of the bacterial chromosomes towards a physical balance, with the minima and maxima corresponding to the known or putative ori and ter and being about half chromosome separated in most of the bacteria studied. A nonparametric method based on wavelet transformation was employed to perform significance tests for the predicted loci. Conclusions: The wavelet approach can reliably predict the ori and ter regions and the bacterial chromosomes have a strong tendency towards a physical balance between ori and ter.
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【期刊论文】Genomic Diversification among Archival Strains of Salmonella enterica Serovar Typhimurium LT7
刘树林, Gui-Rong Liu, , Kelly Edwards, Abraham Eisenstark, Ying-Mei Fu, Wei-Qiao Liu, Kenneth E. Sanderson, Randal N. Johnston, and Shu-Lin Liu, *
JOURNAL OF BACTERIOLOGY, Apr. 2003, p.2131-2142,-0001,():
-1年11月30日
To document genomic changes during long periods of storage, we analyzed Salmonella enterica serovar Typhimurium LT7, a mutator strain that was previously reported to have higher rates of mutations compared to other serovar Typhimurium strains such as LT2. Upon plating directly from sealed agar stabs that had been stocked at room temperature for up to four decades, many auxotrophic mutants derived from LT7 gave rise to colonies of different sizes. Restreaking from single colonies consistently yielded colonies of diverse sizes even when we repeated single-colony isolation nine times. Colonies from the first plating had diverse genomic changes among and even within individual vials, including translocations, inversions, duplications, and point mutations, which were detected by rare-cutting endonuclease analysis with pulsed-field gel electrophoresis. Interestingly, even though the colony size kept diversifying, all descendents of the same single colonies from the first plating had the same sets of detected genomic changes. We did not detect any colony size or genome structure diversification in serovar Typhimurium LT7 stocked at 70℃ or in serovar Typhimurium LT2 stocked either at 70℃ or at room temperature. These results suggest that, although colony size diversification occurred during rapid growth, all detected genomic changes took place during the storage at room temperature and were carried over to their descendents without further changes during rapid growth in rich medium. We constructed a genomic cleavage map on the LT7 strain that had been stocked at 70 ℃ and located all of the detected genomic changes on the map. We speculated on the significance of mutators for survival and evolution under environmentally stressed conditions.
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刘树林, Suneetha Alokam, Shu-Lin Liu, Kamal Said, and Kenneth E. Sanderson*
JOURNAL OF BACTERIOLOGY, Nov. 2002, p.6190-6197,-0001,():
-1年11月30日
Genomic rearrangements (duplications and inversions) in enteric bacteria such as Salmonella enterica serovar Typhimurium LT2 and Escherichia coli K12 are frequent (10-3 to 10-5) in culture, but in wild-type strains these genomic rearrangements seldom survive. However, inversions commonly survive in the terminus of replication (TER) region, where bidirectional DNA replication terminates; nucleotide sequences from S. enterica serovar Typhimurium LT2, S. enterica serovar Typhi CT18, E. coli K12, and E. coli O157:H7 revealed genomic inversions spanning the TER region. Assuming that S. enterica serovar Typhimurium LT2 represents the ancestral genome structure, we found an inversion of 556 kb in serovar Typhi CT18 between two of the 25 IS200 elements and an inversion of about 700 kb in E. coli K12 and E. coli O157:H7. In addition, there is another inversion of 500 kb in E. coli O157:H7 compared with E. coli K12. PCR analysis confirmed that all S. enterica serovar Typhi strains tested, but not strains of other Salmonella serovars, have an inversion at the exact site of the IS200 insertions. We conclude that inversions of the TER region survive because they do not significantly change replication balance or because they are part of the compensating mechanisms to regain chromosome balance after it is disrupted by insertions, deletions, or other inversions.
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