Comparative Genomic and Protein Sequence Analyses of a Complex System Controlling Bacterial Chemotaxis

The ILR1-like family of hydrolase genes was initially isolated inArabidopsis thalianaand is thought to help regulate levels of free indole-3-acetic-acid.We have investigated how this family has evolved in dicotyledon, monocotyledon and gymnosperm species by employing the GenBank and TIGR databases to retrieve orthologous genes. The relationships among these sequences were assessed employing phylogenomic analyses to examine molecular evolution and phylogeny. The members of the ILR1-like family analysed were ILL1, ILL2, ILL3, ILL6, ILR1 and IAR3. Present evidence suggests that IAR3 has undergone the least evolution and is most conserved. This conclusion is based on IAR3 having the largest number of total interspecific orthologues, orthologous species and unique orthologues. Although less conserved than IAR3, DNA and protein sequence analyses of ILL1 and ILR1 suggest high conservation. Based on this conservation, IAR3, ILL1 and ILR1 may have had major roles in the physiological evolution of ‘higher’ plants. ILL3 is least conserved, with the fewest orthologous species and orthologues. The monocotyledonous orthologues for most family-members examined have evolved into two separate molecular clades from dicotyledons, indicating active evolutionary change. The monocotyledon clades are: (a) those possessing a putative endoplasmic reticulum localizing signal; and (b) those that are putative cytoplasmic hydrolases. IAR3, ILL1 and ILL6 are all highly orthologous to a gene in the gymnospermPinus taeda, indicating an ancient enzymatic activity. No orthologues could be detected inChlamydomonas, moss and fern databases.

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Classification and phylogeny of Hexactinellida (Porifera)

Canadian Journal of Zoology ◽

10.1139/z05-174 ◽

2006 ◽

Vol 84 (2) ◽

pp. 195-204 ◽

Cited By ~ 21

Author(s):

H M Reiswig

Keyword(s):

Nucleic Acid ◽

Protein Sequence ◽

Classification Scheme ◽

Sequence Analyses ◽

Present Scheme ◽

Fossil Material ◽

Species Descriptions

Development of the present classification scheme of the class Hexactinellida was delayed because authors of the early species descriptions did not figure their specimens and few of them had access to compound microscopes necessary to visualize characters important in determining relationships. When microscopic information on spicule symmetry became available, Wyville Thomson in 1868 recognized the distinctive triaxial symmetry of the group and named it Vitrea. Schmidt's 1870 name, Hexactinellidae, was without the contamination associated with Thomson's Vitrea, and gained widespread support. Through a series of proposals and refinements, the present scheme recognizes two main lineages, Amphidiscophora and Hexasterophora, differing in shape and type of their microscleres. Since these structures are generally not retained in fossil material, paleontologists have long had an independent classification for hexactinellids, but the trend to unify the systems is now nearly complete. Hypotheses on phylogeny of the group remain virtually dependent upon scarce paleontological information, pending data from nucleic acid and protein sequence analyses that are not yet available for unravelling relationships among hexactinellids.

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Genomic Analysis ofAcinetobacter baumanniiA118 by Comparison of Optical Maps: Identification of Structures Related to Its Susceptibility Phenotype

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01595-10 ◽

2011 ◽

Vol 55 (4) ◽

pp. 1520-1526 ◽

Cited By ~ 18

Author(s):

Maria Soledad Ramirez ◽

Mark D. Adams ◽

Robert A. Bonomo ◽

Daniela Centrón ◽

Marcelo E. Tolmasky

Keyword(s):

Drug Resistance ◽

Antibiotic Resistance ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Restriction Maps ◽

Sequence Analyses ◽

Resistant Phenotype ◽

Optical Map ◽

Optical Maps

ABSTRACTAcinetobacter baumanniiA118, a naturally competent clinical isolate, is unusually susceptible to several antibiotics. Comparison of the optical map of strain A118 within silico-generated restriction maps of sequenced genomes and sequence analyses showed that the AbaR region, commonly found inserted within thecomMgene in other isolates, is missing in strain A118, which could in part explain the susceptible phenotype exhibited by this isolate. These comparative studies also showed differences in regions where genes coding for functions that may be involved in drug resistance or susceptibility are located. Further sequencing demonstrated thatcatandblaADC, namedblaADC-55, are present but that atet(A) gene usually found in other strains is not. In addition,carOandpbp2, which may play a role in susceptibility to carbapenems, are present in strain A118. These findings support the idea thatA. baumanniistrains possess multiple mechanisms that contribute to antibiotic resistance, and the presence of some of them is not sufficient for a resistant phenotype. The results shown here indicate that optical mapping is a useful tool for preliminary comparative genomic analysis.

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Comparative Ribosomal Protein Sequence Analyses of a Phylogenetically Defined Genus, Pseudomonas, and Its Relatives

International Journal of Systematic Bacteriology ◽

10.1099/00207713-45-2-268 ◽

1995 ◽

Vol 45 (2) ◽

pp. 268-273 ◽

Cited By ~ 13

Author(s):

K. OCHI

Keyword(s):

Ribosomal Protein ◽

Protein Sequence ◽

Sequence Analyses

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MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization

BMC Bioinformatics ◽

10.1186/1471-2105-7-459 ◽

2006 ◽

Vol 7 (1) ◽

Cited By ~ 1

Author(s):

Carol L Ecale Zhou ◽

Marisa W Lam ◽

Jason R Smith ◽

Adam T Zemla ◽

Matthew D Dyer ◽

...

Keyword(s):

Protein Sequence ◽

Protein Characterization ◽

Sequence Analyses ◽

Evidence Integration

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Bacillus niabensis sp. nov., isolated from cotton-waste composts for mushroom cultivation

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64178-0 ◽

2007 ◽

Vol 57 (8) ◽

pp. 1909-1913 ◽

Cited By ~ 18

Author(s):

Soon-Wo Kwon ◽

Seon-Young Lee ◽

Byung-Yong Kim ◽

Hang-Yeon Weon ◽

Jung-Bong Kim ◽

...

Keyword(s):

Dna Hybridization ◽

Gene Sequence ◽

Novel Species ◽

Comparative Genomic ◽

Rrna Gene ◽

Mushroom Cultivation ◽

Rrna Gene Sequence ◽

Sequence Analyses ◽

Genomic Analyses ◽

Cotton Waste

A group of five bacilli, designated strains 4T12, 4T19T, 5M45, 5M53 and 5T52, isolated from cotton-waste composts for mushroom cultivation, were examined. These strains were Gram-positive, aerobic, motile, spore-forming rods. 16S rRNA gene sequence analyses revealed that the isolates belonged to the genus Bacillus, showing the highest levels of similarity (approx. 96.6–96.9 %) with respect to Bacillus herbersteinensis DSM 16534T. The values for DNA–DNA hybridization (approx. 85–96 %) among these five strains revealed that they belong to the same species. The major menaquinone present was MK-7 and the predominant cellular fatty acids were anteiso-C15 : 0 (approx. 24.5–33.9 %) and C16 : 0 (approx. 15.1–34.1 %). The DNA G+C contents were 37.7–40.9 mol%. On the basis of physiological, biochemical, chemotaxonomic and comparative genomic analyses, the five isolates represent a novel species of the genus Bacillus, for which the name Bacillus niabensis sp. nov. is proposed. The type strain is 4T19T (=KACC 11279T =DSM 17723T).

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