Abstract:
:The evolutionary relationship within prokaryotes is examined based on signature sequences (defined as conserved inserts or deletions shared by specific taxa) and phylogenies derived from different proteins. Archaebacteria are indicated as being monophyletic by a number of proteins related to the information transfer processes. In contrast, for several other highly conserved proteins, common signature sequences are present in archaebacteria and Gram-positive bacteria, whereas Gram-negative bacteria are indicated as being distinct. For these proteins, archaebacteria do not form a phylogenetically distinct clade but show polyphyletic branching within Gram-positive bacteria. A closer relationship of archaebacteria to Gram-positive bacteria in comparison with Gram-negative bacteria is generally seen for the majority of the available gene/ protein sequences. To account for these results and the fact that both archaebacteria and Gram-positive bacteria are prokaryotes surrounded by a single cell membrane, I propose that the primary division within prokaryotes is between monoderm prokaryotes (surrounded by a single membrane) and diderm prokaryotes (i.e. all true Gram-negative bacteria containing both an inner cytoplasmic membrane and an outer membrane). This proposal is consistent with both cell morphology and signature sequences in different proteins. The monophyletic nature of archaebacteria for some genes, and their polyphyletic branching within Gram-positive bacteria as suggested by others, is critically examined, and several explanations, including derivation of archaebacteria from Gram-positive bacteria in response to antibiotic selection pressure, are proposed. Signature sequences in proteins also indicate that the low-G+C Gram-positive bacteria are phylogenetically distinct from the high-G+C Gram-positive group and that the diderm prokaryotes (i.e. Gram-negative bacteria) appear to have evolved from the latter group. Protein phylogenies and signature sequences also show that all eukaryotic cells have received significant gene contributions from both an archaebacterium and a Gram-negative eubacterium. Thus, the hypothesis that archaebacteria and eukaryotes shared a common ancestor exclusive of eubacteria is not supported. These observations provide evidence for an alternate view of the evolutionary relationship among living organisms that is different from the currently popular three-domain proposal.
journal_name
Mol Microbioljournal_title
Molecular microbiologyauthors
Gupta RSdoi
10.1046/j.1365-2958.1998.00978.xsubject
Has Abstractpub_date
1998-08-01 00:00:00pages
695-707issue
3eissn
0950-382Xissn
1365-2958journal_volume
29pub_type
杂志文章,评审abstract::Era is a low-molecular-weight GTPase essential for Escherichia coli viability. The gene encoding Era is found in the rnc operon, and the synthesis of both RNase III and Era increases with growth rate. Mutants that are partially defective in Era GTPase activity or that are reduced in the synthesis of wild-type Era beco...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1046/j.1365-2958.1998.00719.x
更新日期:1998-02-01 00:00:00
abstract::Although the aerobic degradation of aromatic compounds has been extensively studied in many microorganisms, the anaerobic mineralization of the aromatic ring is a more recently discovered microbial capacity on which very little information is available from facultative anaerobic bacteria. In this issue of Molecular Mi...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2958.2005.04937.x
更新日期:2005-12-01 00:00:00
abstract::Enteropathogenic Escherichia coli (EPEC) is a leading cause of infant diarrhoea. EPEC mediates several effects on host epithelial cells, including activation of signal-transduction pathways, cytoskeletal rearrangement along with pedestal and attaching/effacing lesion formation. It has been previously shown that the EP...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2958.1996.tb02619.x
更新日期:1996-04-01 00:00:00
abstract::The Crp/Fnr family of transcriptional regulators play central roles in transcriptional control of diverse physiological responses, and are activated by a surprising diversity of mechanisms. MrpC is a Crp/Fnr homolog that controls the Myxococcus xanthus developmental program. A long-standing model proposed that MrpC ac...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1111/mmi.14378
更新日期:2019-11-01 00:00:00
abstract::The nucleotide sequence of trkA, a gene encoding a surface component of the constitutive K(+)-uptake systems TrkG and TrkH from Escherichia coli, was determined. The structure of the TrkA protein deduced from the nucleotide sequence accords with the view that TrkA is peripherally bound to the inner side of the cytopla...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2958.1993.tb01714.x
更新日期:1993-08-01 00:00:00
abstract::The genes encoding cholera toxin, the principal virulence factor of Vibrio cholerae, are part of the circular single-stranded DNA genome of CTXphi. In toxigenic V. cholerae strains, the CTXphi genome is typically found in integrated arrays of tandemly arranged CTX prophages. Infected cells that lack a chromosomal inte...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1046/j.1365-2958.2001.02517.x
更新日期:2001-07-01 00:00:00
abstract::Bacteroides fragilis toxin (BFT) is a protein secreted by enterotoxigenic (ETBF) strains of B. fragilis. BFT is synthesized as a proprotein (proBFT) that is predicted to be a lipoprotein and that is cleaved into two discrete fragments by a clostripain-like protease called fragipain (Fpn). In this study, we obtained ev...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1111/mmi.14616
更新日期:2020-09-29 00:00:00
abstract::The genes ftsE and ftsX are organized in one operon together with ftsY. FtsY codes for the receptor of the signal recognition particle (SRP) that functions in targeting a subset of inner membrane proteins. We have found no indications for a structural relationship between FtsE/X and FtsY. Evidence is presented that Ft...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1046/j.1365-2958.1999.01245.x
更新日期:1999-02-01 00:00:00
abstract::The group A streptococcus (GAS) causes a variety of human diseases, including toxic shock syndrome and necrotizing fasciitis, which are both associated with significant mortality. Even the superficial self-limiting diseases caused by GAS, such as pharyngitis, impose a significant economic burden on society. GAS can ca...
journal_title:Molecular microbiology
pub_type: 杂志文章,评审
doi:10.1111/j.1365-2958.2007.05649.x
更新日期:2007-04-01 00:00:00
abstract::Bacillus subtilis SpoIIE is a Ser protein phosphatase whose action on the phosphoprotein SpoIIAA triggers the cell type-specific activation of a sporulation transcription factor. Here we report that SpoIIE displays sequence similarity to the PP2C family of eukaryotic Ser/Thr protein phosphatases, and that residues com...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1046/j.1365-2958.1997.1801552.x
更新日期:1997-01-01 00:00:00
abstract::The exosporium is the outermost layer of the Bacillus anthracis spore. The predominant protein on the exosporium surface is BclA, a collagen-like glycoprotein. BclA is incorporated on the spore surface late in the B. anthracis sporulation pathway. A second collagen-like protein, BclB, has been shown to be surface-expo...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2958.2008.06420.x
更新日期:2008-10-01 00:00:00
abstract::Cytochrome c biogenesis describes the posttranslational pathway for the conversion of pre-apocytochrome c into the mature holocytochrome c. It involves an unknown number of consecutive biochemical steps, including translocation of the precursor polypeptide and haem into the periplasm and the covalent linkage between t...
journal_title:Molecular microbiology
pub_type: 杂志文章,评审
doi:10.1111/j.1365-2958.1994.tb00988.x
更新日期:1994-04-01 00:00:00
abstract::The Bacillus subtilis genome encodes three apparent lipoyl ligase homologues: yhfJ, yqhM and ywfL, which we have renamed lplJ, lipM and lipL respectively. We show that LplJ encodes the sole lipoyl ligase of this bacterium. Physiological and biochemical characterization of a ΔlipM strain showed that LipM is absolutely ...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2958.2011.07597.x
更新日期:2011-04-01 00:00:00
abstract::The outer membrane channel TolC is a key component of multidrug efflux and type I secretion transporters in Escherichia coli. Mutational inactivation of TolC renders cells highly susceptible to antibiotics and leads to defects in secretion of protein toxins. Despite impairment of various transport functions, no growth...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2958.2010.07245.x
更新日期:2010-08-01 00:00:00
abstract::Proteic toxin-antitoxin (TA) loci were first identified in bacterial plasmids, and they were regarded as involved in stable plasmid maintenance by a so-called 'addiction' mechanism. Later, chromosomally encoded TA loci were identified and their function ascribed to survival mechanisms when bacteria were subjected to s...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2958.2006.05027.x
更新日期:2006-02-01 00:00:00
abstract::The unfolded protein response (UPR) is an important stress signalling pathway involved in the cellular development and environmental adaptation of fungi. We investigated the importance of the UPR pathway in the pathogenicity of the plant necrotrophic fungus Alternaria brassicicola, which causes black spot disease on a...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2958.2010.07522.x
更新日期:2011-03-01 00:00:00
abstract::We report here the cloning of the arginine repressor gene argR of Bacillus stearothermophilus and the characterization and purification to homogeneity of its product. The deduced amino acid sequence of the 16.8-kDa ArgR subunit shares 72% identity with its mesophilic homologue AhrC of Bacilus subtilis. Sequence analys...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1046/j.1365-2958.1997.4781845.x
更新日期:1997-07-01 00:00:00
abstract::Aspergillus nidulans was used as a model organism to investigate the fungal propionate metabolism and the mechanism of growth inhibition by propionate. The fungus is able to grow slowly on propionate as sole carbon and energy source. Propionate is oxidized to pyruvate via the methylcitrate cycle. The key enzyme methyl...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1046/j.1365-2958.2000.01737.x
更新日期:2000-03-01 00:00:00
abstract::When fungi grow on plant or insect surfaces coated with wax polyesters that protect against pathogens, the fungi generally form aerial hyphae to contact the surfaces. Aerial structures such as hyphae and conidiophores are coated with hydrophobins, which are surface-active proteins involved in adhesion to hydrophobic s...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2958.2005.04803.x
更新日期:2005-09-01 00:00:00
abstract::A library of genomic DNA fragments from Haemophilus influenzae type b (Hib) DL42 was constructed in plasmid pBR322, transformed into Escherichia coli strain RR1, and screened for recombinant clones with haemin-binding activity by plating onto haemin-containing agar. Expression of haemin-binding activity by clones corr...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2958.1991.tb02107.x
更新日期:1991-02-01 00:00:00
abstract::The cytochrome d complex of Escherichia coli is a heterodimer located in the bacterial cytoplasmic membrane, where it functions as a terminal oxidase of the aerobic respiratory chain. The topology of each of the two subunits of the cytochrome d complex was analysed by the genetic method involving alkaline phosphatase ...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2958.1991.tb02097.x
更新日期:1991-10-01 00:00:00
abstract::The classic expression pattern of the Fis global regulatory protein during batch culture consists of a high peak in the early logarithmic phase of growth, followed by a sharp decrease through mid-exponential growth phase until Fis is almost undetectable at the end of the exponential phase. We discovered that this patt...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2958.2007.05916.x
更新日期:2007-10-01 00:00:00
abstract::In the budding yeast Saccharomyces cerevisiae, the preservation of the mating competent haploid (a or alpha) and the mating incompetent diploid (a/alpha) is necessary to prevent aneuploidy. Once haploid cells respond to pheromone, the mating-specific signal transduction pathway is activated, and the MAP kinase Fus3 ph...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1046/j.1365-2958.2002.03213.x
更新日期:2002-11-01 00:00:00
abstract::We have found a simple relationship between bacterial growth rate and the translation elongation rate. Thus, for a set of defined ribosomal protein S12 mutations which reduce the efficiency of the ternary complex ribosome interaction (and restrict the frequency of translational errors) there is a linear relationship b...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2958.1993.tb01118.x
更新日期:1993-01-01 00:00:00
abstract::Type II restriction enzymes are paired with modification enzymes that protect type II restriction sites from cleavage by methylating them. A plasmid carrying a type II restriction-modification gene complex is not easily replaced by an incompatible plasmid because loss of the former leads to cell death through chromoso...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1046/j.1365-2958.2001.02436.x
更新日期:2001-05-01 00:00:00
abstract::Protein translocation across the bacterial cytoplasmic membrane has been studied extensively in Escherichia coli. The identification of the components involved and subsequent reconstitution of the purified translocation reaction have defined the minimal constituents that allowed extensive biochemical characterization ...
journal_title:Molecular microbiology
pub_type: 杂志文章,评审
doi:10.1046/j.1365-2958.2000.01980.x
更新日期:2000-07-01 00:00:00
abstract::The Ca(2+)-dependent protein phosphatase calcineurin is an important regulator of ion transporters from many organisms, including the Saccharomyces cerevisiae vacuolar Ca(2+)/H(+) exchanger Vcx1p. In yeast and plants, cation/H(+) exchangers are important in shaping cytosolic Ca(2+) levels involved in signal transducti...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2958.2004.04332.x
更新日期:2004-11-01 00:00:00
abstract::TOL plasmid pWW0 of Pseudomonas putida contains two operons that specify a pathway for the degradation of aromatic hydrocarbons. The upper pathway operon encodes the enzymes for the oxidation of toluene/xylenes to benzoate/toluates, and the metacleavage pathway operon encodes the enzymes for the further oxidation of t...
journal_title:Molecular microbiology
pub_type: 杂志文章,评审
doi:10.1111/j.1365-2958.1993.tb01222.x
更新日期:1993-09-01 00:00:00
abstract::Each year, several million tons of dimethylsulfoniopropionate (DMSP) are produced by marine phytoplankton and bacteria as an important osmolyte to regulate their cellular osmosis. Microbial breakdown of DMSP to the volatile gas dimethylsulfide (DMS) plays an important role in global biogeochemical cycles of the sulphu...
journal_title:Molecular microbiology
pub_type: 评论,杂志文章
doi:10.1111/mmi.14230
更新日期:2019-06-01 00:00:00
abstract::Computer analysis of the crystallographic structure of the A subunit of Escherichia coli heat-labile toxin (LT) was used to predict residues involved in NAD binding, catalysis and toxicity. Following site-directed mutagenesis, the mutants obtained could be divided into three groups. The first group contained fully ass...
journal_title:Molecular microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2958.1994.tb01266.x
更新日期:1994-10-01 00:00:00