Forgot your password?
New user?
New Window Opens on the Secret Life of Microbes: Scientists Develop First Microbial Profiles of Ecosystems
CAS announces the release of SciFinder Scholar for Mac OS X
Press Releases
Press Releases
| Check out our New Publishers' Select for Free Articles |
Archives of Microbiology (v.194, #1)
Phylogenetic perspectives of nitrogen-fixing actinobacteria by Maher Gtari; Faten Ghodhbane-Gtari; Imen Nouioui; Nicholas Beauchemin; Louis S. Tisa (pp. 3-11).
It was assumed for a long time that the ability to catalyze atmospheric nitrogen (diazotrophy) has a narrow distribution among actinobacteria being limited to the genus Frankia. Recently, the number of nitrogen fixation (nifH) genes identified in other non-Frankia actinobacteria has dramatically increased and has opened investigation on the origin and emergence of diazotrophy among actinobacteria. During the last decade, Mycobacterium flavum, Corynebacterium autotrophicum and a fluorescent Arthrobacter sp. have been reported to have nitrogenase activity, but these studies have not been further verified. Additional reports of nitrogen fixation by Agromyces, Microbacterium, Corynebacterium and Micromonospora isolated from root nodules of leguminous and actinorhizal plants have increased. For several actinobacteria, nitrogen fixation was demonstrated by the ability to grow on nitrogen-free medium, acetylene reduction activity, 15N isotope dilution analysis and identification of a nifH gene via PCR amplification. Moreover, the analyses of draft genome sequences of actinobacteria including Slackia exigua, Rothia mucilaginosa and Gordonibacter pamelaeae have also revealed the presence of nifH-like sequences. Whether these nifH sequences are associated with effective nitrogen fixation in these actinobacteria taxa has not yet been demonstrated. These genes may be vertically or horizontally transferred and be silent sequences. These ideas merit further investigation. This minireview presents a phylogenetic comparison of nitrogen fixation gene (nifH) with the aim of elucidating the processes underlying the evolutionary history of this catalytic ability among actinobacteria.
Keywords: Actinobacteria; Diazotrophy; Phylogeny
Development of a semi-high-throughput growth assay for the filamentous actinobacteria Frankia by Teal Furnholm; Nicholas Beauchemin; Louis S. Tisa (pp. 13-20).
Filamentous bacteria pose unique challenges for testing multiple variables or growth parameters limiting the use of high-throughput methods. A semi-high-throughput growth assay system was developed to overcome these obstacles and validated for the filamentous actinobacteria Frankia. The 24-well plate assay was versatile for testing multiple growth medium parameters and provided reproducible results across wells and between plates. Under conditions of increased complexity, statistical analysis demonstrated that the variance was dependent on the experimental parameters and not the assay system. The 24-well plate assay was shown to be multipurpose for testing numerous variables on cell growth or other biological properties.
Keywords: Actinobacteria; Hyphal growth; Screening protocol; Semi-high-throughput
Growth and development of Frankia spp. strain CcI3 at the single-hypha level in liquid culture by Ying Huang; David R. Benson (pp. 21-28).
Filamentous actinobacteria from the genus Frankia grow by hyphal tip extension and branching. The growth kinetics and branching pattern of Frankia are not well studied, especially at the early stages of mycelial development. Here, we compare the growth of Frankia sp. strain CcI3 in liquid cultures with and without proteose peptone #3 (PP3) using time-lapse photomicrography and image analysis. Individual hyphae showed a pseudolinear increase in length at early stages of development, whereas at the mycelial level, the aggregate length of hyphae described an exponential rate before slowing. Growth based on optical density or microscopic observations was similar in medium with or without PP3. However, PP3 altered the pattern of mycelial development by increasing branching. Distances between the hyphal apex and first branches were on average shorter in PP3-containing media. The final interbranch distances were also shorter in PP3 medium indicating that hyphae tended to branch earlier and more often when supplemented with PP3 to give a more compact mycelium. Vesicle development in nitrogen-fixing cultures limited cell expansion as a result of vesicles truncating growth on new branches. The results provide some explanation for the growth kinetics of Frankia and some indication of how growth rates may be improved.
Keywords: Actinomycete; Filamentous; Vesicle; Hyphae
Organization of nif gene cluster in Frankia sp. EuIK1 strain, a symbiont of Elaeagnus umbellata by Chang Jae Oh; Ho Bang Kim; Jitae Kim; Won Jin Kim; Hyoungseok Lee; Chung Sun An (pp. 29-34).
The nucleotide sequence of a 20.5-kb genomic region harboring nif genes was determined and analyzed. The fragment was obtained from Frankia sp. EuIK1 strain, an indigenous symbiont of Elaeagnus umbellata. A total of 20 ORFs including 12 nif genes were identified and subjected to comparative analysis with the genome sequences of 3 Frankia strains representing diverse host plant specificities. The nucleotide and deduced amino acid sequences showed highest levels of identity with orthologous genes from an Elaeagnus-infecting strain. The gene organization patterns around the nif gene clusters were well conserved among all 4 Frankia strains. However, characteristic features appeared in the location of the nifV gene for each Frankia strain, depending on the type of host plant. Sequence analysis was performed to determine the transcription units and suggested that there could be an independent operon starting from the nifW gene in the EuIK strain. Considering the organization patterns and their total extensions on the genome, we propose that the nif gene clusters remained stable despite genetic variations occurring in the Frankia genomes.
Keywords: nif gene cluster; Frankia sp. EuIK1; Elaeagnus umbellata ; Sequence analysis; Gene organization
Identification of TTA codon containing genes in Frankia and exploration of the role of tRNA in regulating these genes by Arnab Sen; Subarna Thakur; Asim K. Bothra; Saubashya Sur; Louis S. Tisa (pp. 35-45).
The TTA codon, one of the six available codons for the amino acid leucine, is the rarest codon among the high GC genomes of Actinobacteria including Frankia. This codon has been implicated in various regulatory mechanisms involving secondary metabolism and morphological development. TTA-mediated gene regulation is well documented in Streptomyces coelicolor, but that role has not been investigated in other Actinobacteria including Frankia. Among the various Actinomycetes with a GC content of more than 70%, Frankia genomes had the highest percentages of TTA-containing genes ranging from 5.2 to 10.68% of the genome. In contrast, TTA-bearing genes comprised 1.7, 3.4 and 4.1% of the Streptomyces coelicolor, S. avermitilis and Nocardia farcinia genomes, respectively. We analyzed their functional role, evolutionary significance, horizontal acquisition and the codon-anticodon interaction. The TTA-bearing genes were found to be well represented in metabolic genes involved in amino acid transport and secondary metabolism. A reciprocal Blast search reveal that many of the TTA-bearing genes have orthologs in the other Frankia genomes, and some of these orthologous genes also have a TTA codon in them. The gene expression level of TTA-containing genes was estimated by the use of the codon adaption index (CAI), and the CAI values were found to have a positive correlation with the GC3 (GC content at the 3rd codon position). A full-atomic 3D model of the leucine tRNA recognizing the TTA (UUA) codon was generated and utilized for in silico docking to determine binding affinity in codon-anticodon interaction. We found a proficient codon-anticodon interaction for this codon which is perhaps why so many genes hold on to this rare codon without compromising their translational efficiency.
Keywords: Actinomycetes; Frankia ; TTA codon; Expression; tRNA; Docking
Lectin genes in the Frankia alni genome by Petar Pujic; Pascale Fournier; Nicole Alloisio; Anne-Emmanuelle Hay; Joelle Maréchal; Stéphanie Anchisi; Philippe Normand (pp. 47-56).
Frankia alni strain ACN14a’s genome was scanned for the presence of determinants involved in interactions with its host plant, Alnus spp. One such determinant type is lectin, proteins that bind specifically to sugar motifs. The genome of F. alni was found to contain 7 such lectin-coding genes, five of which were of the ricinB-type. The proteins coded by these genes contain either only the lectin domain, or also a heat shock protein or a serine-threonine kinase domain upstream. These lectins were found to have several homologs in Streptomyces spp., and a few in other bacterial genomes among which none in Frankia EAN1pec and CcI3 and two in strain EUN1f. One of these F. alni genes, FRAAL0616, was cloned in E. coli, fused with a reporter gene yielding a fusion protein that was found to bind to both root hairs and to bacterial hyphae. This protein was also found to modify the dynamics of nodule formation in A. glutinosa, resulting in a higher number of nodules per root. Its role could thus be to permit binding of microbial cells to root hairs and help symbiosis to occur under conditions of low Frankia cell counts such as in pioneer situations.
Keywords: Alnus ; Binding; Frankia ; Genome; Lectin; Nodulation