Microbial & comparative genomics最新文献_第6页

A large family of eukaryotic-like protein Ser/Thr kinases of Myxococcus xanthus, a developmental bacterium. 黄粘球菌真核样蛋白丝氨酸/苏氨酸激酶大家族，一种发育性细菌

Microbial & comparative genomics Pub Date : 2000-01-01 DOI: 10.1089/10906590050179783

S Inouye, R Jain, T Ueki, H Nariya, C Y Xu, M Y Hsu, B A Fernandez-Luque, J Munoz-Dorado, E Farez-Vidal, M Inouye

{"title":"A large family of eukaryotic-like protein Ser/Thr kinases of Myxococcus xanthus, a developmental bacterium.","authors":"S Inouye, R Jain, T Ueki, H Nariya, C Y Xu, M Y Hsu, B A Fernandez-Luque, J Munoz-Dorado, E Farez-Vidal, M Inouye","doi":"10.1089/10906590050179783","DOIUrl":"https://doi.org/10.1089/10906590050179783","url":null,"abstract":"Myxococcus xanthus is a gram-negative bacterium that forms multicellular fruiting bodies upon starvation. Here, we demonstrate that it contains at least 13 eukaryotic-like protein Ser/Thr kinases (Pkn1 to Pkn13) individually having unique features. All contain the kinase domain of approximately 280 residues near the N-terminal end, which share highly conserved features in eukaryotic Ser/Thr kinases. The kinase domain is followed by a putative regulatory domain consisting of 185 to 692 residues. These regulatory domains share no significant sequence similarities. The C-terminal regions of 11 kinases contain at least 1 transmembrane domain, suggesting that they function as transmembrane sensor kinases. From the recent genomic analysis, protein Ser/Thr kinases were found in various pathogenic bacteria and coexist with protein His kinases. Phylogenetic analysis of these Ser/Thr kinases reveals that all bacterial Ser/Thr kinases were evolved from a common ancestral kinase together with eukaryotic Tyr and Ser/Thr kinases. Coexistence of both Ser/Thr and His kinases in some organisms may be significant in terms of functional differences between the two kinases. We argue that both kinases are essential for some bacteria to adapt optimally to severe environmental changes.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/10906590050179783","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21913739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 50

The mammalian FEN-1 locus: structure and conserved sequence features. 哺乳动物FEN-1基因座的结构与保守序列特征。

Microbial & comparative genomics Pub Date : 2000-01-01 DOI: 10.1089/OMI.1.2000.5.173

Z. Karanjawala, X. Shi, C. Hsieh, M. Lieber

引用次数: 8

MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products. MultiFun，大肠杆菌K-12基因产物的多功能分类方案。

Microbial & comparative genomics Pub Date : 2000-01-01 DOI: 10.1089/OMI.1.2000.5.205

M. Serres, M. Riley

{"title":"MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products.","authors":"M. Serres, M. Riley","doi":"10.1089/OMI.1.2000.5.205","DOIUrl":"https://doi.org/10.1089/OMI.1.2000.5.205","url":null,"abstract":"An enriched classification system for cellular functions of gene products of Escherichia coli K-12 was developed based on the initial classification by Riley. In the new classification scheme, MultiFun, cellular functions are divided into 10 major categories: Metabolism, Information Transfer, Regulation, Transport, Cell Processes, Cell Structure, Location, Extra-chromosomal Origin, DNA Site, and Cryptic Gene. These major categories are further sub-divided into a hierarchical scheme. Two thousand nine hundred twenty-two gene products of E. coli K-12 were assigned to one or more functions depending on the role they play in the cell. Functional assignments were made to 66% of E. coli gene products, ranging from 1 to 16 assignments per gene product. The expansion of cellular function categories and the assignment to more than one category (multifunction) provides a more complete description of the gene products and their roles and hence better reflects the functional complexity of organisms. We believe this classification system will be useful in the field of genome analysis, both for annotation purposes and for comparative studies. The functional classification scheme and the cellular function assignments made to E. coli gene products can be accessed from the web at the databases GenProtEC (http://genprotec.mbl.edu) and EcoCyc (http://www.ecocyc.org).","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/OMI.1.2000.5.205","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60514615","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 161

Causal analysis of CpG suppression in the Mycoplasma genome. 支原体基因组CpG抑制的原因分析。

Microbial & comparative genomics Pub Date : 2000-01-01 DOI: 10.1089/10906590050145267

M Goto, T Washio, M Tomita

{"title":"Causal analysis of CpG suppression in the Mycoplasma genome.","authors":"M Goto, T Washio, M Tomita","doi":"10.1089/10906590050145267","DOIUrl":"https://doi.org/10.1089/10906590050145267","url":null,"abstract":"Some bacterial genomes are known to have low CpG dinucleotide frequencies. While their causes are not clearly understood, the frequency of CpG is suppressed significantly in the genome of Mycoplasma genitalium, but not in that of Mycoplasma pneumoniae. We compared orthologous gene pairs of the two closely related species to analyze CpG substitution patterns between these two genomes. We also divided genome sequences into three regions: protein-coding, noncoding, and RNA-coding, and obtained the CpG frequencies for each region for each organism. It was found that the observed/expected ratio of CpG dinucleotides is low in both the protein-coding and noncoding regions; while that ratio is in the normal range in the RNA-coding region. Our results indicate that CpG suppression of the Mycoplasma genome is not caused by (1) biased usage amino acid; (2) biased usage of synonymous codon; or (3) methylation effects by the CpG methyltransferase in the genomes of their hosts. Instead, we consider it likely that a certain global pressure, such as genome-wide pressure for the advantages of DNA stability or replication, has the effect of decreasing CpG over the entire genome, which, in turn, resulted in the biased codon usage.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/10906590050145267","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21845088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 14

Nucleotide sequence and phylogenetic analysis of long terminal repeats of human endogenous retrovirus K family (HERV-K) on human chromosomes. 人内源性逆转录病毒K家族(HERV-K)染色体长末端重复序列的核苷酸序列和系统发育分析。

Microbial & comparative genomics Pub Date : 2000-01-01 DOI: 10.1089/OMI.1.2000.5.121

H. Kim, J. Y. Choi, W. Lee, K. Jang, B. Hyun

引用次数: 2

The power of comparison. 比较的力量。

Microbial & comparative genomics Pub Date : 2000-01-01 DOI: 10.1089/10906590050179738

G A Evans

引用次数: 0

Mammalian cochlear genes and hereditary deafness. 哺乳动物耳蜗基因与遗传性耳聋。

Microbial & comparative genomics Pub Date : 2000-01-01 DOI: 10.1089/10906590050179747

B S Shastry

引用次数: 6

Comparative analysis of Chlamydia bacteriophages reveals variation localized to a putative receptor binding domain. 衣原体噬菌体的比较分析显示变异定位于一个假定的受体结合域。

Microbial & comparative genomics Pub Date : 2000-01-01 DOI: 10.1089/OMI.1.2000.5.223

T. Read, C. Fraser, R. Hsia, P. Bavoil

{"title":"Comparative analysis of Chlamydia bacteriophages reveals variation localized to a putative receptor binding domain.","authors":"T. Read, C. Fraser, R. Hsia, P. Bavoil","doi":"10.1089/OMI.1.2000.5.223","DOIUrl":"https://doi.org/10.1089/OMI.1.2000.5.223","url":null,"abstract":"Three recently discovered ssDNA Chlamydia-infecting microviruses, phiCPG1, phiAR39, and Chp2, were compared with the previously characterized phage from avian C. psittaci, Chp1. Although the four bacteriophages share an identical arrangement of their five main genes, Chpl has diverged significantly in its nucleotide and protein sequences from the other three, which form a closely related group. The VP1 major viral capsid proteins of phiCPG1 and phiAR39 (from guinea pig-infecting C. psittaci and C. pneumoniae, respectively) are almost identical. However, VP1 of ovine C. psittaci phage Chp2 shows a high rate of nucleotide sequence change localized to a region encoding the \"IN5\" loop of the protein, thought to be a potential receptor-binding site. Phylogenetic analysis suggests that the ORF4 replication initiation protein is evolving faster than the other phage proteins. phiCPG1, phiAR39, and Chp2 are closely related to an ORF4 homolog inserted in the C. pneumoniae chromosome. This sequence analysis opens the way toward understanding the host-range and evolutionary history of these phages.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/OMI.1.2000.5.223","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60514632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 33

Analysis of the expressed genome of the lone star tick, Amblyomma americanum (Acari: Ixodidae) using an expressed sequence tag approach. 用表达序列标记法分析孤星蜱，Amblyomma americanum(蜱螨:伊蚊科)的表达基因组。

Microbial & comparative genomics Pub Date : 2000-01-01 DOI: 10.1089/10906590050179774

C A Hill, J A Gutierrez

{"title":"Analysis of the expressed genome of the lone star tick, Amblyomma americanum (Acari: Ixodidae) using an expressed sequence tag approach.","authors":"C A Hill, J A Gutierrez","doi":"10.1089/10906590050179774","DOIUrl":"https://doi.org/10.1089/10906590050179774","url":null,"abstract":"An expressed sequence tag (EST) approach was used to study the genome of two developmental stages of the lone star tick, Amblyomma americanum. cDNA libraries were constructed from the larval and adult stages of A. americanum. In total, 1942 ESTs were sequenced (1462 adult ESTs and 480 larval ESTs) and analyzed using bioinformatic programs. Contig assembly using the CAPII program revealed 11% and 15% redundancy of sequences in the larval and adult ESTs, respectively. Of the 1942 ESTs, 1738 sequences were considered quality sequences and of these, 771 or approximately 44.4% of the sequences were putatively identified based on amino acid identity using the protein Basic Local Alignment Search Tool (BLAST) algorithm. Putatively identified sequences were classified according to their predicted gene function. In total, 967 sequences, or 55.6% of the quality sequences, had limited or no protein similarity to previously identified gene products. Sequences lacking protein homology were analyzed using an automated sequence annotation system for predicted protein characteristics such as open reading frames, signal peptides, protein motifs, and transmembrane regions. In this paper we describe the sequencing of the largest number of ESTs obtained from an arachnid species to date and the subsequent detailed analysis of these sequences.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/10906590050179774","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21913738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 28

Sequencing of the Francisella tularensis strain Schu 4 genome reveals the shikimate and purine metabolic pathways, targets for the construction of a rationally attenuated auxotrophic vaccine. 土拉菌菌株Schu 4基因组测序揭示了shikimate和嘌呤代谢途径，这是构建合理减毒的营养缺陷疫苗的目标。

Microbial & comparative genomics Pub Date : 2000-01-01 DOI: 10.1089/10906590050145249

J Karlsson, R G Prior, K Williams, L Lindler, K A Brown, N Chatwell, K Hjalmarsson, N Loman, K A Mack, M Pallen, M Popek, G Sandström, A Sjöstedt, T Svensson, I Tamas, S G Andersson, B W Wren, P C Oyston, R W Titball

{"title":"Sequencing of the Francisella tularensis strain Schu 4 genome reveals the shikimate and purine metabolic pathways, targets for the construction of a rationally attenuated auxotrophic vaccine.","authors":"J Karlsson, R G Prior, K Williams, L Lindler, K A Brown, N Chatwell, K Hjalmarsson, N Loman, K A Mack, M Pallen, M Popek, G Sandström, A Sjöstedt, T Svensson, I Tamas, S G Andersson, B W Wren, P C Oyston, R W Titball","doi":"10.1089/10906590050145249","DOIUrl":"https://doi.org/10.1089/10906590050145249","url":null,"abstract":"Francisella tularensis is the etiological agent of tularemia, a serious disease in several Northern hemisphere countries. The organism has fastidious growth requirements and is very poorly understood at the genetic and molecular levels. Given the lack of data on this organism, we undertook the sample sequencing of its genome. A random library of DNA fragments from a highly virulent strain (Schu 4) of F. tularensis was constructed and the nucleotide sequences of 13,904 cloned fragments were determined and assembled into 353 contigs. A total of 1.83 Mb of nucleotide sequence was obtained that had a G+C content of 33.2%. Genes located on plasmids pOM1 and pNFL10, which had been previously isolated from low virulence strains of F. tularensis, were absent but all of the other known F. tularensis genes were represented in the assembled data. F. tularensis Schu4 was able to grow in the absence of aromatic amino acids and orthologues of genes which could encode enzymes in the shikimate pathway in other bacteria were identified in the assembled data. Genes that could encode all of the enzymes in the purine biosynthetic and most of the en- zymes in the purine salvage pathways were also identified. This data will be used to develop defined rationally attenuated mutants of F. tularensis, which could be used as replacements for the existing genetically undefined live vaccine strain.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/10906590050145249","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21844607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 54