Phylogenetic diversity of bacterial endophytes

F ISH 技术的探针要求必须具有较好的特异性、灵敏性和良好的组织渗透性。

根据需要合成的DNA或RNA寡核苷酸探针可识别靶序列内一个碱基的变化, 能够用酶学或化学方法进行非放射性标记。

F ISH 技术不仅能提供静止的实验结果, 还可以动态地观察流动水体中的微生物种群变化, 因此FISH 技术被用于监测环境中微生物在时间或空间上的动态变化, 以帮助人们理解环境中微生物种群的组成和生长动力学。

FISH 的首次应用是在1980 年，Bauman [1]等用荧光染料直接标记探针RNA的3'端，检测到了特异的DNA，1988 年Giovnanoni [2]等将FISH 技术引进到了细菌学，他第一次用放射性同位素标记已知的rRNA寡核苷酸探针进行细菌的显微镜观察，随后该技术在系统发育微生物学、微生物生态学、微生物的诊断和周围环境的研究中得到了迅速的发展。

目前在单一样品( 如纯培养菌种) 检测中的应用已十分普遍，准确度较高［3，4］，但在复杂样品( 如活性污泥) 检测中的应用仍不成熟，易受到样品中所含杂质的影响，出现假阳性或假阴性信号［5］。

本文采用细菌通用探针EUB338，结合DAPI全细胞染色技术，探讨了针对活性污泥样品的荧光原位杂交实验方法，并对自发荧光和真实信号的辨别要点进行了讨论。

[7] Bauman J G J ，Wiegant J ，V an Duijn P . Cytochemical hybridization with fluorochromelabeled RNA. Ⅲ. Increased sensitivity by the use of anti-fluorescein antibodies［J］. Histochemistry，1981，73（4）: 181-193［8］Giovannoni S J ，DeLong E F ，Olsen G J ，Pace N R . Phylogenetic group-specific oligodeoxynucleotide Probes for identification of single microbial cells［J］. Bacteriol，1988，170（21）: 720-726.［3］万春黎. 同步脱氮脱硫工艺生物强化及种群动态分析初探［M］. 哈尔滨:哈尔滨工业大学，2006.123-127［4］任艳红. 降解五氯酚厌氧生物反应器微生物种群结构的分子特性研究［M］. 浙江: 浙江大学，2004.342-145［5］王明义，袁晓燕，宋雪珍，等. 荧光原位杂交法在检测硫酸盐还原菌中的应用［J］.中国现代医学杂志，2008，18( 3) :302-304.荧光原位杂交技术结合分子生物学的精确性和显微镜的可视性, 可进行微生物的空间分布情况分析和特征性微生物的鉴定与定量分析。

叶绿体系统发育基因组学的研究进展*张韵洁，李德铢＊＊（中国科学院昆明植物研究所生物多样性与生物地理学重点实验室，云南昆明650201）摘要：系统发育基因组学是由系统发育研究和基因组学相结合产生的一门崭新的交叉学科。

近年来，在植物系统发育研究中，基于叶绿体基因组的系统发育基因组学研究优势渐显端倪，为一些分类困难类群的系统学问题提出了解决方案，但同时也存在某些问题。

本文结合近年来叶绿体系统发育基因组学研究中的一些典型实例，讨论了叶绿体系统发育基因组学在植物系统关系重建中的价值和应用前景，并针对其存在问题进行了探讨，其中也涉及了新一代测序技术对叶绿体系统发育基因组学的影响。

关键词：系统发育基因组学；叶绿体基因组；新一代测序技术；长枝吸引中图分类号：Q75，Q949文献标识码：A文章编号：2095－0845（2011）04－365－11 Advances in Phylogenomics Based on Complete Chloroplast GenomesZHANG Yun-Jie，LI De-Zhu＊＊（Key Laboratory of Biodiversity and Biogeography，Kunming Institute of Botany，Chinese Academy of Sciences，Kunming650201，China）Abstract：Phylogenomics is a new synthesized discipline which combines genomics with phylogenetics．Phylogenom-ics based on chloroplast genomes has shown many great advantages in plant phylogenetic research in recent years，providing resolutions for phylogeny of some taxonomically difficult groups of plants．However，there are some prob-lems coming along with chloroplast phylogenomics as well．In this review，the application prospects and potential problems of chloroplast phylogenomics in plant phylogenetic reconstruction were discussed based on recent phylog-enomic case studies．The influence of next-generation sequencing on chloroplast phylogenomics was also discussed．Key words：Phylogenomics；Chloroplast genome；Next-generation sequencing；Long-branch attraction地球上的生命形式多种多样，它们因有着共同的进化历史而有着或近或远的渊源。

Phylogenetic Classification of Prokaryotic and Eukaryotic Sir2-like ProteinsRoy A.Frye 1Pittsburgh V.A.Medical Center (132L),Department of Pathology,University of Pittsburgh,Pittsburgh,Pennsylvania 15240Received May 31,2000Sirtuins (Sir2-like proteins)are present in pro-karyotes and eukaryotes.Here,two new human sir-tuins (SIRT6and SIRT7)are found to be similar to a particular subset of insect,nematode,plant,and pro-tozoan sirtuins.Molecular phylogenetic analysis of 60sirtuin conserved core domain sequences from a di-verse array of organisms (including archaeans,bacte-ria,yeasts,plants,protozoans,and metazoans)shows that eukaryotic Sir2-like proteins group into four main branches designated here as classes I–IV.Pro-karyotic sirtuins include members of classes II and III.A fifth class of sirtuin is present in gram positive bac-teria and Thermotoga maritima.Saccharomyces cer-evisiae has five class I sirtuins.Caenorhabditis elegans and Drosophila melanogaster have sirtuin genes from classes I,II,and IV.The seven human sirtuin genes include all four classes:SIRT1,SIRT2,and SIRT3are class I,SIRT4is class II,SIRT5is class III,and SIRT6and SIRT7are class IV.©2000Academic PressKey Words:molecular phylogeny;evolution;Sir2;chromatin;aging;DNA stability;epigenetic;NAD me-tabolism;deacetylase.In addition to silencing genes within the silent mating-type loci and telomeric regions the yeast Sir2protein is targeted to the nucleolus (1,2)where it causes several effects such as alteration of chromatin structure (3),gene silencing (4–6),modulation of the meiotic checkpoint (7),decreased recombination of rDNA (8),and a decreased rate of aging (9).All Sir2-like proteins have a sirtuin core domain which contains a series of sequence motifs conserved in organisms ranging from bacteria to humans (10,11).Bacterial,yeast,and mammalian sirtuins are able to metabolize NAD and possibly act as mono-ADP-ribosyltrans-ferases (11,12).The enzymatic function of sirtuins is not yet completely understood but recent reports ofhistone-activated Sir2-mediated NAD metabolism (12,13)and NAD-activated Sir2-mediated histone deacety-lation (13,14)suggest a possible coupled reciprocal activation mechanism involving interactions of Sir2with NAD and the N ⑀-acetyl-lysine groups of acety-lated histones.It is possible that an enzymatic mech-anism of this sort that couples binding and metabolism of both NAD and N-linked acetyl groups is a key fea-ture of all sirtuins;however not all sirtuins function physiologically by interacting with acetylated histones because prokaryotes lack histones yet many pro-karyotes possess sirtuins,also some eukaryotic sir-tuins appear to be cytoplasmic and thus not accessible to histones (15,16).Here the conserved sirtuin core domain sequences from a variety of prokaryotic and eukaryotic organisms are compared and it is found that the eukaryotic sirtuin sequences can be grouped into four main classes.MATERIALS AND METHODSCharacterization of human SIRT6and ing the human SIRT4sequence as a probe,a BLAST search of human sequences in GenBank yielded several expressed sequence tags (ESTs)for SIRT6and SIRT7and the genomic sequence for SIRT6.The Clontech human spleen Marathon cDNA library served as a source for cDNA clones that were isolated using PCR primers de-rived from the GenBank sequences and the Clontech AP1primer.Pfu-turbo high-fidelity thermostable polymerase from Stratagene was used for amplification and the PCR products were cloned into the InVitrogen pcr4TOPO cloning vector and sequenced with an ABI PRISM 377.BLASTP similarity score analysis.The full length amino acid sequences for each sirtuin was compared with the sequence of the other sirtuin using the “Blast 2sequences”utility at the NCBI Blast website (/gorf/bl2.html).For the D.mel3se-quence the currently available GenBank Drosophila genomic DNA sequence has a gap of 17codons just upstream of the region encoding the conserved FGE motif.Molecular phylogenetic analysis.Most of the 60sirtuin sequences listed in Table 1were obtained from GenBank,some of the sequences were obtained from preliminary sequence data from The Institute for Genomic Research (TIGR)accessed via the “Microbial Genomes:Finished and Unfinished”Blast website (/Microb_blast/unfinishedgenome.html).In the TIGR-released prelim-inary DNA sequence data for the B.per sirtuin gene there are three1To whom correspondence should be addressed at V.A.Medical Center (132L),University Drive C,Pittsburgh,PA 15240.Fax:412-688-6872.E-mail:frye01@.Biochemical and Biophysical Research Communications 273,793–798(2000)doi:10.1006/bbrc.2000.3000,available online at onX’s designating indefinite bases;in the analysis for this paper these three X’s were provisionally substituted with G’s because the molec-ular phylogeny analysis software(see below)would not process se-quences with X’s.For some sequences the putative protein-encoding sequences were derived by splicing together segments of genomic sequence;putative splice sites were determined using the Gene Finder software(:9331/gene-finder/gf.html) and by assessing homology to similar known sirtuin cDNAs.The conserved core domain sequences were aligned by ClustalW and further adjustments to the alignment were made manually using the SeqPUP program.The multiple sequence alignment data was con-verted to Phylip format and the60aligned sequences were analyzed by the MOLPHY:protML program(17)and the resulting“outtree”dataset was converted to a treefile using the PHYLIP:consensus program.The treefile was converted to an unrooted dendrogram using the PHYLIP:drawtree program.The MOLPHY and PHYLIP programs were utilized via the Pasteur Institute Bioweb site(http:// bioweb.pasteur.fr/).RESULTSSIRT6and SIRT7human sirtuin genes.The hu-man sirtuin gene family is comprised of seven known members.Each sirtuin contains a conserved core do-main,in some instances additional N-terminal or C-terminal sequence is present(Fig.1A).For some of the human sirtuin genes(SIRTs1,2,3,4,and6)the genomic sequence is available(Table1).A SIRT5-like pseudogene is present on chromosome1p31.2-32.1 (GenBank Accession No.AL157407bases46500–48000).The SIRT6gene is on chromosome19p13.3 between CDC34and D19S325.The SIRT7gene has been mapped(as Unigene EST cluster Hs.184447)to chromosome17q between D17S784and qTEL.The SIRT6and SIRT7cDNAs encode proteins with pre-dicted Mrof39.1and44.9KDa,respectively.The SIRT6and SIRT7sequences are much more similar to each another than they are to Sir2(BLASTP similarity scores:SIRT6:SIRT7ϭ178,SIRT6:Sir2ϭ61,SIRT7: Sir2ϭ53).The SIRT6and SIRT7sequences are highly similar to some sirtuins from Drosophila melanogaster, Caenorhabditis elegans,Oryza sativa(rice),Arabidop-sis thaliana,and the protozoan malaria parasite Plas-modium falciparum(Fig.1B).Drosophila homologues of human sirtuins.The genomic sequence of Drosophila melanogaster has re-cently been determined(18).A search of this Drosoph-ila database revealedfive sirtuin genes(Table1).Thesefive Drosophila sirtuins are homologues offive of the human sirtuins.Very high BLASTP similarity scores are seen when each Drosophila sirtuin is com-pared with the corresponding human homologue (D.mel1:SIRT1ϭ440,D.mel2:SIRT2ϭ353,D.mel3: SIRT4ϭ263, D.mel4:SIRT6ϭ294,and D.mel5: SIRT7ϭ364).These data suggest that sirtuins from organisms representing diverse phyla can be grouped into distinct sequence-related classes.Molecular phylogeny of prokaryotic and eukaryotic sirtuin core domain sequences.Molecular phyloge-netic analysis software,the MOLPHY:protML pro-gram(17),was used to analyze the aligned conserved core domains of60sirtuins from a variety of pro-karyotes and eukaryotes.This yielded an unrooted tree diagram with the eukaryotic sirtuins grouped into four main branches(Fig.2).Class I:The main branch leading toward Sir2is designated as class I.The yeast Sir2and proteins such as Hst1,SIRT1,C.ele1,and D.mel1form a subgroup called class Ia.The yeast Hst2and proteins that in-clude SIRT2,SIRT3,and D.mel2form the subgroup class Ib.The yeast Hst3and Hst4genes are subgroup Ic;the currently available data indicates thatsirtuins FIG.1.SIRT6and SIRT7are two new members of the human sirtuin family with high homology to certain eukaryotic sirtuins.(A) The placement of the conserved core domain(darkly shaded)in Sir2 from S.cerevisiae and the seven human sirtuins(sizes range from SIRT5at33.9kDa to SIRT1at81.7kDa).(B)Aligned amino acid sequences comparing human SIRT6and SIRT7with similar sirtuins from fruitfly,nematode,two plants,and the malaria parasite.Black shading indicates residues that are conserved in at least50%of the sequences.The portrayed sequence segments all begin with the initiation methionine except for SIRT7and D.mel5which begin at the55th and29th amino acids respectively.See Table1for accession information on sequences.of this Ic subgroup are found only in yeasts.Class I sirtuins are not present in prokaryotes.Class II:The human SIRT4and the fruitfly D.mel3are class II sirtuins (Fig.2).The two class II sirtuin genes of Caenorhabditis elegans are both located on the same cosmid clone,perhaps the result of a gene dupli-cation event.Interestingly,some bacteria have class II sirtuin genes (e.g.,Streptomyces coelicolor A3(2),My-cobacterium avium,and Bordetella pertussis ).Class III:The human SIRT5is a class III sirtuin (Fig.2).Candida albicans and Plasmodium falcipa-rum also have class III sirtuins.Most bacterial sirtuin sequences are of class III type;in addition to those noted in Table 1there are other bacterial class III sequences present in the TIGR database (e.g.,se-quences from Pseudomonas aeruginosa and Pasteu-rella multocida ).There are some completely-sequenced bacterial genomes which lack sirtuin genes,these in-clude:Rickettsia prowazekii,Borrelia burgdorferi,Chlamydia muridarum,Chlamydia pneumoniae,Chlamydia trachomati,Mycoplasma genitalium,Chlamydophila pneumoniae,Synechocystis,Neisseria meningitidis,Treponema pallidum,and Ureaplasma urealyticum.Several archaeans (e.g.,Archaeoglobus fulgidus,Aeropyrum pernix,Pyrococcus furiosus,Pyro-coccus horikoshii,and Pyrococcus abyssi )have class III sequences but the completely-sequenced archaeans Methanobacterium thermoautotrophicum and Meth-anococcus jannaschii lack sirtuin genes.Class IV:The SIRT6and SIRT7sirtuins are both class IV sirtuins.The class IV sirtuins are further subdivided into class IVa (SIRT6, D.mel4, C.ele4,P.Fal2,O.sat,and A.tha)and class IVb (SIRT7and D.mel5).Class IV sirtuins are not present in pro-karyotes.Class U:Several Firmicute (gram positive)bacteria and Thermotoga maritima have sirtuin genes with se-quence motifs that seem to be intermediate between classes II and III and the classes I and IV;this undif-ferentiated form of sirtuin gene is called “class U.”The gram positive bacterium Streptomyces coelicolor A3(2)has a class II sirtuin (S.coe1)and a second sirtuin (S.coe2)that is class U.Characteristic sequence motifs of the various classes of sirtuins.Figure 3illustrates the specific amino acid sequence motifs that characterize the different classes of sirtuins.The core domain sequences of seven members from each of the five classes were first shaded to indicate intraclass-conserved resi-dues and then the five grouped sequence sets were aligned to facilitate interclass comparison.There are several short motifs of conserved amino acids present within the sirtuin core domain;these include GAGISXXXGIPXXR,PXXXH,TQNID,HG,two sets of CXXC that may be a zinc finger domain (10),FGE,GTS,and (I/V)N (Fig.3).In class III sirtuins theTABLE 1Sirtuin Sequence Abbreviations,Sirtuin Class Designa-tion,Source Organism,and GenBank Accession Numbers (Genomic Regular Font/cDNA Italic Font)Abbreviation (Class)Organism (Genomic #/cDNA #)A.act (III)Actinobacillus actinomycetemcomitans (AF006830)A.aeo (III)Aquifex aeolicus (AE000776)A.ful1(III)Archaeoglobus fulgidus (AE000987)A.ful2(III)Archaeoglobus fulgidus (AE001098)A.per (III)Aeropyrum pernix (AP000062)A.tha (IVa)Arabidopsis thaliana (AB009050)B.per (II)Bordetella pertussis (TIGR)B.sub (U)Bacillus subtilis (Z99109)C.ace (U)Clostridium acetabutylicum (TIGR)C.alb1(Ia)Candida albicans (O59923)C.alb2(Ib)Candida albicans (CAA22018)C.alb3(Ic)Candida albicans (TIGR)C.alb4(III)Candida albicans (TIGR)C.dif (U)Clostridium difficile (TIGR)C.ele1(Ia)Caenorhabditis elegans (Z70310)C.ele2(II)Caenorhabditis elegans (Z50177)C.ele3(II)Caenorhabditis elegans (Z50177)C.ele4(IVa)Caenorhabditis elegans (U97193)C.jej (III)Campylobacter jejuni (AL139077)D.mel1(Ia)Drosophila melanogaster (AE003639/AF068758)D.mel2(Ib)Drosophila melanogaster (AE003730)D.mel3(II)Drosophila melanogaster (AE003435)D.mel4(IVa)Drosophila melanogaster (AE003686)D.mel5(IVb)Drosophila melanogaster (AE003768)D.rad (III)Deinococcus radiodurans (AAF09608)E.col (III)Escherichia coli (AE000212)E.fae (U)Enterococcus faecalis (TIGR)Hst1(Ia)Saccharomyces cerevisiae (U39041)Hst2(Ib)Saccharomyces cerevisiae (U39063)Hst3(Ic)Saccharomyces cerevisiae (U39062)Hst4(Ic)Saccharomyces cerevisiae (Z48784)H.pyl (III)Helicobacter pylori (AE001545)L.maj1(Ib)Leishmania major (AL160493/L40331)L.maj2(II)Leishmania major (AL117324)M.avi1(II)Mycobacterium avium (TIGR)M.avi2(III)Mycobacterium avium (TIGR)M.tub (III)Mycobacterium tuberculosis (Z95584)O.sat (IVa)Oryza sativa (AF159133)P.aby (III)Pyrococcus abyssi (AJ248286)P.fal1(III)Plasmodium falciparum (AL049185)P.fal2(IVa)Plasmodium falciparum (TIGR)P.hor (III)Pyrococcus horikoshii (AP000004)S.aur (U)Staphylococcus aureus (M32103)S.coe1(II)Streptomyces coelicolor A3(2)(AL121596)S.coe2(U)Streptomyces coelicolor A3(2)(AL035205,AL035206)S.pom1(Ia)Schizosaccharomyces pombe (AL035637)S.pom2(Ib)Schizosaccharomyces pombe (AL121807)S.pom3(Ic)Schizosaccharomyces pombe (AL136499/AF173939)S.typ (III)Salmonella typhimurium (U89687)Sir2(Ia)Saccharomyces cerevisiae (X01419)SIRT1(Ia)Homo sapiens (AL133551/NM_012238)SIRT2(Ib)Homo sapiens (AC011455/NM_012237)SIRT3(Ib)Homo sapiens (AF015416/NM_012239)SIRT4(II)Homo sapiens (AC003982/NM_012240)SIRT5(III)Homo sapiens (NM-012241)SIRT6(IVa)Homo sapiens (AC006930/AF233396)SIRT7(IVb)Homo sapiens (AF233395)T.bru (Ib)Trypanosoma brucei (AF102869)T.mar (U)Thermotoga maritima (AE001726)Y.pes (III)Yersinia pestis (TIGR)GAGISXXXGIPXXR motif is usually GAGISAESGI-PTFR whereas in class II it is GAGISTESGIPDYR.Sirtuins of classes U,I,and IV also have GIPD within this motif,thus the presence of GIPT within this motif is indicative of a class III sequence.In class IV sequences there is a GVWTL motif present four residues C-terminal to the GAGISTXXGIPDFR motif.In class II sequences there is an RXRY-WARXXXGW motif present 27residues C-terminal to the GAGISTESGIPDYR motif.In sequences of classes II,III,and U,the PXXXH motif is PNXXH while in the eukaryotic class I and IV sequences a T or S usually follows the P.The HG motif is of interest because the point mutation that changes HG to YG causes loss of sirtuin-mediated ADP-ribosylation and deacetylation (11,12,14)and it converts yeast SIR2to a dominant negative gene (12).The HG motif is strictly conserved in all known sirtuins.In class Ia the HG motif reads CHG,in class Ib it is AHG,in class Ic (and in most non-class I sirtuins)it is LHG.The three residues located five residues C-terminal to the GTS motif are rather useful in differenti-ating between the types of sirtuins.The three residues usually seen at this position for each class and subclass are:Ia(PVA or PVS),Ib(PFA),Ic(GVK),U(PAA),II(SGY),III(PAA),IVa(PXX),and IVb(KKY).DISCUSSIONAlthough some prokaryotes lack Sir2-like proteins it appears that sirtuins are present in all eukaryotes.The five sirtuin genes of the completely-sequenced Sac-charomyces cerevisiae are all of class I subtypes;thus this yeast has evolved to survive in the absence of non-class I sirtuins.However,except for yeasts most eukaryotic organisms seem to harbor an assortment of both non-class I and class I sirtuin genes.Many types of eukaryotes have class II and class IV sirtuins.In addition to the human,insect,nematode,and Leish-mania class II sirtuins described here (Table 1),partial-length sequence data indicate that class II sirtuins are present in Trypanosoma brucei (TIGR_5691|T.brucei_27H6.TJ),a mold fungus (As-pergillus nidulans AA788405),and plants (A.thaliana N38434,Soybean AW395917).The class IV sirtuins are also widely distributed and seen in vertebrate,insect,nematode,protist,and plant lifeforms (Fig.1).In summary,the currently available data indicate that class I,class II,and class IV sirtuins could be present in all metazoan organisms and that some protists also possess these classes of sirtuins.The genomic sequence data sets for D.melanogaster and C.elegans are complete and no class III sirtuin sequences are found;thus these two organismsareFIG.2.The molecular phylogeny of sirtuins.An alignment of the conserved domains of 60sirtuin sequences was analyzed by the MOLPHY:protML program and the PHYLIP:consensus and PHYLIP:drawtree programs were then used to construct this unrooted tree diagram.See Table 1for accession information on sequences.examples of metazoans which lack class III sirtuins.The class III sirtuin is the most widely distributed form found in prokaryotes,thus it may be a very ancient version of the sirtuin gene.Because class III genes are found in most non-gram-positive bacteria and most archaeans it is unclear in which prokaryotic domain this gene originated.The class III sirtuin gene may have been present prior to the divergence of the two prokaryotic domains,otherwise the class III gene might have traversed the boundary between Archaea and Bacteria via lateral gene transfer.It seems incon-gruous that prokaryotes,Candida albicans,and mam-mals have a class III gene while some eukaryotes (e.g.,S.cerevisiae,C.elegans,and D.melanogaster )lack a class III gene.Current theory on the origin of eu-karyotes has modified the endosymbiont hypothesis of Margulis (19)by postulating the fusion of a bacterium with an archaean (20–22).A preliminary model for the evolution and distribution of eukaryotic sirtuins can be proposed (Fig.4)in which the first eukaryote may have acquired sirtuin genes from each of its prokaryotic parents,these genes were of the types which are known to occur in prokaryotes i.e.class U,class II,and class III.Protozoans and metazoans from diverse phyla have class I and class IV sirtuins,so these types of sirtuins must have developed at an early stage of eu-karyotic evolution.Thus this model postulates that an early eukaryote possessed all four types of sirtuinsandFIG.3.The conservation of specific sequence motifs within the different classes of sirtuins.Seven sirtuins from each class (U,I,II,III,and IV)are aligned and residues that are intraclass-conserved (in at least five of the seven sequences)are shaded black.Numbers in parentheses indicate amino acid residues present in variable regions that have been omitted to condense the size of the figure.that later some eukaryotes lost one (e.g.,Drosophila and C.elegans which lack class III)or more (e.g.,S.cerevisiae which lacks classes II,III,and IV)of the non-class I sirtuins.This model predicts that all four classes of sirtuins are likely to be present in some organisms (e.g.,echinoderms and chordates)that are phylogenetically similar to lifeforms that were ances-tral to vertebrates.Much current research effort is aimed at determin-ing the specific molecular interactions and physiologi-cal functions of the sirtuins in both prokaryotic and eukaryotic organisms.To date the most extensively-studied sirtuin is the yeast Sir2protein itself which is a class Ia sirtuin that appears to function via an inter-action with NAD and acetylated histones to cause mod-ification of chromatin structure (12–14).The physiolog-ical functions and molecular interactions associated with other classes of sirtuins are still largely unknown.It is likely that particular classes and subclasses of sirtuins will be found to interact physiologically with particular types and subtypes of biomolecules that serve as sirtuin modulators and sirtuin substrates.Perhaps this classification of the sirtuins into specific sequence-defined groups will provide a framework to help integrate research from diverse biological systems on the molecular signaling pathways and physiological functions associated with these various classes of Sir2-like proteins.ACKNOWLEDGMENTThis work was supported by the Competitive Pilot Project Fund of the Veterans Affairs Stars and Stripes Healthcare Network.REFERENCES1.Gotta,M.,Strahl-Bolsinger,S.,Renauld,H.,Laroche,T.,Kennedy,B.K.,Grunstein,M.,and Gasser,S.M.(1997)EMBO J.16,3243–3255.2.Straight,A.F.,Shou,W.,Dowd,G.J.,Turck,C.W.,Deshaies,R.J.,Johnson,A.D.,and Moazed,D.(1999)Cell 97,245–256.3.Fritze,C.E.,Verschueren,K.,Strich,R.,and Easton Esposito,R.(1997)EMBO 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47卷 2期2007年4月4日微生物学报Acta Microbio logica Sinica 47(2):313~3184April 2007基金项目:国家 973项目 (2002AA001036);国家自然科学基金(50208006)*通讯作者。

Tel Fax:86 451 86282008;E mail:rnq@作者简介:赵阳国(1975-),男,山东人,博士,从事废水处理与微生物分子生态学研究。

E mail:yg.zhao@ 收稿日期:2006 07 31;接受日期:2006 09 22;修回日期:2006 11 13有机污染物对水体真细菌群落结构的影响赵阳国,任南琪*,王爱杰,万春黎(哈尔滨工业大学市政环境工程学院 哈尔滨 150090)摘 要:为了揭示有机污染物对环境真细菌组成和多样性的影响,应用末端限制性片段长度多态性(tRFLP)和16S rDNA 文库技术并结合水质分析方法,比较分析了松花江流域内受不同程度有机污染的4个水体及其沉积物中真细菌的群落结构。

tRFLP 分析表明各水体及底泥均呈现较为复杂的群落结构模式,不同底泥群落形成的末端限制性片段(TRF)图谱具有很高的相似性,但随着污染程度的加强,部分类群明显富集,而且在水样组和泥样组内,群落结构的相似性同水质相似性是一致的,主成分分析(PC A )显示水样和泥样中的真细菌TRF 形成不同的群。

16S rDNA 文库分析表明松花江哈尔滨段底泥中真细菌分布于10个门,Proteobacteria 门占优势,达群落总数的21 92%( Proteobacteria 亚门占10 96%),而有机染污物严重超标的生活污水排污道底泥中的微生物多样性较低,分布于7个门,Proteobacteria 门为优势群,占群落的47 37%( Proteobacteria 亚门占21 05%, ! Proteobacteria 亚门占15 79%)。

Bacterial Communities in Bioreactors Bacterial communities in bioreactors play a crucial role in various industrial and environmental processes. These communities, also known as biofilms, are complex and dynamic ecosystems consisting of diverse microbial populations. Understanding the composition, structure, and function of these bacterial communities is essential for optimizing bioreactor performance and harnessingtheir potential for biotechnological applications. In this article, we will explore the significance of bacterial communities in bioreactors from multiple perspectives, including their role in wastewater treatment, bioremediation, and bioprocessing. From the perspective of wastewater treatment, bacterial communities in bioreactors are instrumental in removing organic pollutants and nutrients from wastewater. These communities consist of various bacterial species that work synergistically to degrade organic matter and convert nitrogen and phosphorus compounds into less harmful forms. The metabolic activities of these bacteria contribute to the purification of wastewater, making it suitable for discharge or reuse. Moreover, the resilience of these bacterial communities enables them to adapt to fluctuating environmental conditions, ensuring consistent treatment performance over time. This aspect highlights the importance of maintaining a healthy and diverse bacterial community within bioreactors for efficient wastewater treatment. In the context of bioremediation, bacterial communities in bioreactors play a critical role in the degradation of environmental contaminants. Bioremediation processes leverage the metabolic capabilities of bacteria to break down pollutants such as hydrocarbons, heavy metals, and pesticides. By harnessing the diverse enzymatic activities ofdifferent bacterial species, bioreactors can facilitate the transformation of hazardous compounds into less toxic or inert forms. The adaptability of bacterial communities allows them to thrive in contaminated environments and contribute to the restoration of ecosystems. As such, the study and manipulation of these microbial communities are essential for developing effective bioremediation strategies to mitigate environmental pollution. In bioprocessing applications, bacterial communities in bioreactors are utilized for the production of various valuable compounds, including enzymes, biofuels, and pharmaceuticals. Themetabolic diversity of bacterial populations enables the synthesis of a wide range of biochemical products through fermentation processes. By optimizing the composition and dynamics of bacterial communities, bioprocess engineers can enhance product yields, minimize by-product formation, and improve process stability. The intricate interactions within these microbial ecosystems offer opportunities for bioengineering approaches to tailor bacterial communities for specific bioprocessing objectives, ultimately contributing to the sustainable production of bio-based materials. Despite the significant contributions of bacterial communities in bioreactors to various industrial and environmental processes, several challenges and research gaps persist. The complexity of these microbial ecosystems poses difficulties in fully understanding their dynamics and interactions. Furthermore, the influence of operational parameters, such as temperature, pH, and substrate availability, on the stability and performance of bacterial communities requires further investigation. Additionally, the potential emergence of antimicrobial resistance within bioreactor communities raises concerns regarding the long-term sustainability of biotechnological applications reliant on these microbial populations. Addressing these challenges necessitates interdisciplinary efforts encompassing microbiology, bioprocess engineering, environmental science, and bioinformatics. In conclusion, bacterial communities in bioreactors play a multifaceted and indispensable role in various industrial and environmental contexts. Their impact spans from wastewater treatment and bioremediation to bioprocessing, offering diverse opportunities for sustainable resource management and biotechnological innovation. The intricate interplay of microbial species within these communities underscores the need for comprehensive research and technological advancements to harness their potential effectively. By gaining a deeper understanding of bacterial communities in bioreactors and their complex dynamics, we can unlock new possibilities for addressing pressing environmental challenges and advancing bioprocessing capabilities.。

植物繁育系统研究的最新进展和评述何亚平1,2　刘建全13(1中国科学院西北高原生物研究所,西宁　810001)(2中国科学院研究生院,北京　100039)摘　要　植物繁育系统是当今进化生物学研究中最为活跃的领域。

繁育系统是指代表所有影响后代遗传组成的有性特征的总和,主要包括花形态特征、花的开放式样、花各部位的寿命、传粉者种类和频率、自交亲和程度和交配系统,其中交配系统是核心。

我们重点综述了植物有性繁育系统研究中1)传粉模式的多样性,2)从历史发生角度利用系统发育方法检验花性状的演化和繁育系统的生态转变过程,3)近交衰退对植物生殖史的影响及其机制和4)混和交配系统的时空动态、维持机理以及进化趋势的最新研究结果。

总结了繁育系统在研究花适应性、物种形成机制和濒危植物保护生物学中的重要作用。

最后对今后的繁育系统研究提出了两点建议:1)正确理解和使用适应概念,更多地利用人工控制实验来检验花的适应价值和2)将分子技术和生态学结合起来,开展群落水平和种以上水平的繁育系统研究,比较驱动与传粉多样性密切相关的花多样性基因和自花、异花传粉基因的进化与分化,确定繁育系统相互作用中的关键因子。

关键词　繁育系统　进化　系统发育　多样性A REVIEW ON RECENT ADVANCES IN THE STU DIESOF P LANT BREE DING SYSTEMHE Y a-Ping1,2and LI U Jian-Quan13(1Northwest Plateau Institute o f Biology ,the Chinese Academy o f Sciences ,Xining 810001,China )(2Graduate School ,the Chinese Academy o f Sciences ,Beijing 100039,China )Abstract The plant breeding system has become the m ost active and promising area am ong the recent ev olu 2tionary studies.In its definition ,the plant breeding system represents the sum of all sexual characteristics that could possibly in fluence the genetic com position of subsequent generations ,mainly encom passing floral m or 2phological features ,display patterns ,longevity ,species and visitation rates of pollinators ,degree of self-com 2patibility and mating system.Am ong them the mating system is the m ost critical.In this paper we presented a review of the recent advances in the studies of plant breeding systems ,with an em phasis on 1)the diversity of pollination in floral m orphology ,sexual expression ,floral longevity and pollinator ,2)testing the ev olution of the sexual characters and ecological shifts of the breeding system ,such as sex expression ,selfing and outcross 2ing in historical context by an independent phylogenetic approach ,3)effects of inbreeding depression on the plant reproduction cycle and their possible mechanisms ,and 4)spatial and dynamic patterns of the mixed mat 2ing system and their maintenance mechanisms and ev olutionary trends.We further summarized the application of plant breeding system research in the studies of flower adaptation ,speciation and conservation of endangered stly ,for future research ,we suggested that 1)the w ord “adaptation ”should be less used in flower adaptation explanations and m ore valuations should be based on the results of manipulated experiments and 2)both m olecular and ecological methods should be combined to elucidate the plant breeding system at the scale of the community and high tax onomic levels ,to com pare the ev olution and differentiation of the genes which drive flower diversity and control differentiation of the inbreeding and outcrossing ,and to find the determinative factors am ong the interactive relationships in the breeding system.K ey w ords Breeding system ,Ev olution ,Phylogeny ,Diversity 被子植物生活史就是植株-受精卵-植株的循环,但决不是物理的重复,前一过程经历传粉和生殖,其实质是基因型选择,包括传粉、雌雄配子体选择;后一过程经历发育,植株形态建成,实质是表现 收稿日期:2002201216　接受日期:2002207201 基金项目:中国科学院全国优秀博士论文基金、中国科学院知识创新重要方向性项目(K SCX2-SW -121)、中国科学院研究生科学创新项目和国家自然科学基金(30270253)　3通讯作者Author for correspondence E -mail :ljqdxy @植物生态学报　2003,27(2)151～163Acta Phytoecologica Sinica型选择。

Evolutionary Relationships in Phylogenetics Phylogenetics is a fascinating field that seeks to understand the evolutionary relationships between different species. By analyzing genetic data, scientists can construct phylogenetic trees that depict the evolutionary history of various organisms. These trees not only provide insights into the relatedness of different species but also shed light on the patterns and processes of evolution itself.One of the key concepts in phylogenetics is the idea of a common ancestor. According to the theory of evolution, all living organisms are related through a shared ancestry. By studying the genetic similarities and differences between species, scientists can infer the existence of common ancestors and map out the branching points in the evolutionary tree of life. This not only helps us understand how different species are related to each other but also provides clues about the evolutionary processes that have shaped the diversity of life on Earth.The construction of phylogenetic trees relies heavily on the analysis of genetic data. By comparing the DNA sequences of different species, scientists can infer the degree of relatedness between them. This can be done using various computational methods that take into account the patterns of genetic mutations and the principles of evolutionary biology. The resulting phylogenetic trees provide a visual representation of the evolutionary relationships between different species, allowing scientists to make inferences about the timing and patterns of evolutionary divergence.One of the most exciting applications of phylogenetics is in the field of conservation biology. By understanding the evolutionary relationships between different species, scientists can make informed decisions about conservation priorities and strategies. For example, if two species are found to be closely related in terms of their evolutionary history, efforts to conserve one species may also benefit the other. Additionally, phylogenetics can help identify evolutionarily distinct species that are at risk of extinction, allowing conservationists to prioritize their protection.Another important aspect of phylogenetics is the concept of molecular clocks. By analyzing the rate of genetic mutations, scientists can estimate the timing of evolutionary events and the divergence of different lineages. This can provide valuable insights into the timing of key evolutionary events, such as the emergence of major groups of organisms or the colonization of new habitats. Molecular clocks have been used to study a wide range of evolutionary questions, from the timing of human migration out of Africa to the diversification of flowering plants.In conclusion, phylogenetics is a powerful tool for understanding the evolutionary relationships between different species. By analyzing genetic data and constructing phylogenetic trees, scientists can gain insights into the patterns and processes of evolution, as well as make important contributions to fields such as conservation biology and evolutionary biology. The field continues to advance rapidly, driven by technological innovations and the increasing availability of genetic data from a wide range of organisms. As our understanding of phylogenetics grows, so too does our appreciation of the rich tapestry of life on Earth and the interconnectedness of all living things.。