Microbiology Blog: The weblog for microbiologists.

Metabolic Engineering of Microorganisms for Oligosaccharide and Polysaccharide Production

2008-04-15T11:19:00.002+01:00

A huge variety of biopolymers, such as polysaccharides, polyesters, and polyamides, are naturally produced by microorganisms. These range from viscous solutions to plastics and their physical properties are dependent on the composition and molecular weight of the polymer. The genetic manipulation of microorganisms opens up an enormous potential for the biotechnological production of biopolymers with tailored properties suitable for high-value medical application such as tissue engineering and drug delivery.

Microorganisms naturally produce a wide variety of carbohydrate molecules, yet large-scale manufacturing requires production levels much higher than the natural capacities of these organisms. Metabolic engineering efforts generate microbial strains capable of meeting the industrial demand for high synthesis levels. As both oligosaccharide and polysaccharide synthesis are carbon and energy-intensive processes, improved production of these products require similar metabolic engineering strategies. Metabolically engineered strains have successfully produced many carbohydrate products and many unexplored strategies made available from recent progress in systems biology can be used to engineer better microbial catalysts.

Further reading: Microbial Production of Biopolymers and Polymer Precursors

Bacterial Conjugation

2008-04-08T12:48:00.000+01:00

Whatever the route used, horizontal transfer of DNA requires elaborated multi-protein machinery to enable the long and charged nucleic acid polymer to cross the cell envelope barriers. The best-studied system for cell-to-cell DNA translocation is bacterial conjugation. This system can be divided in two discrete specialized modules: the relaxosome, which triggers and takes part in plasmid DNA processing and replication, and a type IV secretion system (T4SS), which impels protein and single-stranded DNA through the membranes. In addition, a coupling protein (CP), linking both modules, and a number of ancillary proteins are needed. Over the last decades research efforts in the field have resulted in the clarification of many aspects of this system and its machinery assembly. In particular, structural biology has provided details of the molecular architecture of several of the pieces involved in this intricate scenario.

Further reading: Plasmids: Current Research and Future Trends

Pasteurellaceae

2008-04-07T16:48:00.001+01:00

Pasteurellaceae comprise a large and diverse family of Gram-negative bacteria with members ranging from important pathogens such as Haemophilus influenzae to commensals of the animal and human mucosa. Information on the biology of these organisms has mushroomed in recent years, driven by the development of novel genetic and molecular methodologies. Since 1995, the family has been expanded from three genera to the current thirteen through the use of new genetic-based classification and identification technologies. Many members of the Pasteurellaceae family make excellent natural models for the study of bacterial pathogenesis and host-pathogen-interactions thus giving valuable insights into related human diseases. Research in this area is at a very exciting stage.

Further reading: Pasteurellaceae: Biology, Genomics and Molecular Aspects

Real-Time PCR

2008-04-07T16:42:00.003+01:00

A number of published reviews on Real-Time PCR have recently been made available as "open-access" papers. These timely and authoritative reviews are written by experts in the field and can be downloaded at: PCR Papers

Further info: PCR Papers

Vibrio cholerae

2008-04-02T12:25:00.001+01:00

Vibrio cholerae, the causative agent of cholera belongs to a group of organisms whose natural habitats are the aquatic ecosystems. The strains that cause cholera epidemics have evolved from non-pathogenic progenitor strains by acquisition of virulence genes, and V. cholerae represents a paradigm for this evolutionary process.

Genomics of Vibrio cholerae and its Evolution
The 4.0 Mbp genome of N16961, an O1 serogroup, El Tor biotype, 7th pandemic strain of V. cholerae, is comprised of two circular chromosomes of unequal size that are predicted to encode a total of 3,885 genes. The genomic sequence of this representative strain has facilitated global experimental approaches that have furthered our understanding of the genetic and phenotypic diversity found within the species V. cholerae. Sequence data have been used to identify horizontally acquired sequences, dissect complex regulatory and signaling pathways, and develop computational approaches to predict patterns of gene expression and the presence of metabolic pathway components. In addition, these data have served as a basis for the construction of microarrays to study the evolution of the organism through comparative genomic analyses. Genomic sequencing of additional strains, subtractive hybridization studies and the introduction of new model systems have also contributed to the identification of novel sequences and pathogenic mechanisms associated with other strains. The sequence of strain N16961 has therefore resulted in an expanded view of the genetic repertoire of V. cholerae and focused our attention on the progressive evolution of this marine bacterium that can also be a human pathogen.

Population Genetics of Vibrio cholerae
The influence of evolutionary forces on the genetic diversity of natural populations of living organisms is the subject matter of population genetics. In the case of Vibrio cholerae, data obtained from detailed molecular studies of large populations of these bacteria have allowed for a better understanding of the epidemiology of diseases due to their presence in humans. The species has a high genetic diversity and a complex image of its population structure. There is also evidence of linkage disequilibrium and frequent intragenic and assortative recombination events in their housekeeping genes. Horizontal transfer of genes in V. cholerae is higher than those reported for Escherichia coli and Salmonella enterica. In spite of the frequent horizontal gene transfer, clonal lineages of Vibrio cholerae might persist for decades. The best example of this is the presence and survival of epidemic and pandemic clones over long periods of time. To date, there are four major genetic lines of toxigenic V. cholerae O1 biotype El Tor: an Australian clone (ET 1); the U.S. Gulf Coast clone (ET 2); the seventh pandemic clone isolated in the South East Asia together with the O139 "Bengal" clone (ET 3); and the clone that caused cholera in Latin America in the 1990's (ET 4). There are also isolated clones that have appeared over time under special conditions, e.g., serogroup O37 that was shown to have limited epidemic potential in the 1960's. Given the close evolutionary relationship between V. cholerae O1 and other non-O1 virulent serotypes and the fact that virulence genes can be transferred horizontally, new pathogenic strains of V. cholerae could arise in the future through the modification of existing clones that have the capacity to spread rapidly, and thus cause outbreaks of disease.

Genetics of Vibrio cholerae Colonization and Motility
Survival of Vibrio cholerae either in the aquatic environment or in the human host is mediated by appropriate expression of factors that control motility, colonization, production of virulence factors, as well as sensing the cell density (quorum sensing). Successful transition of the organism between the aquatic and the host intestinal environments thus depends on the coordinated activity of a number of genes and regulatory circuits.

Genetics of O-antigens, Capsules, and the Rugose Variant of Vibrio cholerae
The human pathogen Vibrio cholerae produces three major cell-surface associated polysaccharides, including (i) lipopolysaccharide (LPS), (ii) capsule, and (iii) rugose exopolysaccharide. While LPS and capsule primarily help the bacterium to evade host defense mechanisms, the rugose exopolysaccharide may aid the bacterium in persisting in the nutrient-deficient aquatic environments.

Genetics and Microbiology of Biofilm Formation by Vibrio cholerae
In nature, most bacteria grow as matrix-enclosed, surface-associated communities known as biofilms. Vibrio cholerae, the causative agent of the disease cholera, forms biofilms on diverse surfaces. This ability to form biofilms appears to be critical for the environmental survival and the transmission of V. cholerae. The molecular mechanisms utilized by V. cholerae to form and maintain biofilms have been investigated by molecular genetic and microscopic approaches and these studies should prove useful in the development of future strategies for predicting and controlling cholera epidemics.

Molecular Ecology of Vibrio cholerae
Although Vibrio cholerae causes human disease, aquatic ecosystems are major habitats of V. cholerae, and all V. cholerae are not pathogenic for humans. V. cholerae represents a paradigm for origination of pathogenic bacteria from environmental nonpathogenic progenitor strains by horizontal transfer of genes. Besides environmental factors which are not precisely defined, bacteriophages, and horizontally transmissible genetic elements have a significant role in the epidemiology and evolution of the pathogen. Recent studies are beginning to reveal the mechanisms associated with the occurrence of seasonal epidemics in endemic areas, waterborne spread of cholera, and the factors that enable the organisms to survive unfavorable conditions in the aquatic environment. The emergence of new epidemic strains, and their enrichment during epidemics of cholera appear to constitute a natural system for the evolution of V. cholerae and genetic elements that mediate horizontal transfer of genes among bacterial strains.

Coordinated Regulation of Gene Expression in Vibrio cholerae
Vibrio cholerae, the causative agent of the severe diarrhoeal disease cholera, has evolved with intricate signal transduction and gene regulatory systems to survive and grow under various environmental conditions. The virulence regulon of V. cholerae, which involves multiple genes working in a coordinated manner, represents a regulatory paradigm for extracellular bacterial pathogens. Availability of the whole genome sequence has allowed microarray based transcriptome analyses of V. cholerae cells isolated directly from cholera patients. Such studies indicate that quite a large number of genes are involved in the disease process and their expression pattern changes as the infection progresses. Further understanding of the process came with the recent discoveries of small noncoding RNAs and intracellular signal molecule c-di-GMP as modulators of gene expression in V. cholerae. Transcriptome analysis has also shed light on synchronized gene expression related to chitin utilization and development of natural competence when the organism exists in the natural aquatic environment. Thus, the survival, evolution and pathogenesis of V. cholerae appear to be controlled by several intricate overlapping regulatory circuits.

Evolutionary Relationships of Pathogenic Clones of Vibrio cholerae
Evolution refers to the differentiation of an ancestral genome into recognizably distinct genomes. Understanding the evolutionary history of an organism can provide insight into how it can be expected to evolve in the future and provide predictions that serve as the basis of where to best focus effort to prevent the emergence of new pathogenic variants. In order to accurately understand the evolutionary history, the methods used for interpreting the genetic variation need to reflect the mechanisms of genetic change. The critical mechanism for deciding how to interpret the genetic relatedness is the amount of recombination. If recombination is rare, then the traditional phylogenetic analysis based on bifurcating trees works well. If recombination is common, then a method that incorporates recombination must be used. Evolutionary relationships among pathogenic clones based on these assessments have been presented and discussed.

Emerging Hybrid Variants of Vibrio cholerae O1
Rapid emergence of genetic variants among toxigenic epidemic strains of Vibrio cholerae, contributes to the intricate epidemiological pattern of cholera. A remarkable event in recent years has been the emergence of strains of V. cholerae O1 which possess traits of both the classical and El Tor biotypes.

Antibiotic Resistance in Vibrio cholerae
Antimicrobial resistance has become a major medical and public health problem as it has direct link with the disease management. Vibrio cholerae, the cholera causing pathogen is increasingly developing resistance towards many antimicrobials used for the treatment of diarrhoea. However, the pattern of resistance differs from country to country. The well-known factor responsible for development and spread of resistance is injudicious use of antimicrobial agents, which is directly related to the stimulation of several mechanisms of resistance. In V. cholerae, several resistance mechanisms such as plasmid encoded resistance, mutation in the quinolones resistance determining regions, integrons, efflux pumps and SXT constins have been established. Considering the importance of drug resistance, quick diagnostic assay methods are available for the identification of multidrug resistant (MDR) V. cholerae. Many new generation antimicrobials were discovered, which are effective against V. cholerae in the in vitro studies. The resistance pattern of V. cholerae to several antimicrobials are not always uniform as it depends on the source of isolation. Vibrios can act as reservoirs of antimicrobial resistance as cross-spread is common in in vitro studies. Promotion of indigenous drugs should be considered in the future and studied in detail for their efficacy.

Further reading: Vibrio cholerae: Genomics and Molecular Biology

Medical mycology

2008-04-01T15:08:00.002+01:00

In recent years the development of new molecular biology tools and the elucidation of whole genome sequences have revolutionized research in medical mycology. Such advances have led to the development of faster, more reliable diagnostic techniques for medically important pathogens such as Candida albicans, Aspergillus fumigatus and Cryptococcus neoformans. In addition they have led to a major breakthrough in the approach for the generation of novel anti-fungal agents.

In a recent book on Medical Mycology a panel of expert international mycologists critically review the most important areas. Topics include: gene expression and regulation, heterozygosity in Candida, molecular diagnosis, regulation of the host-fungal interaction, the development of anti-fungals, signal transduction, and mechanisms of multi-drug resistance.

Further reading: Pathogenic Fungi: Insights in Molecular Biology

Outer Membrane Proteins of H. pylori

2008-04-01T12:30:00.002+01:00

Analysis of the three completed Helicobacter pylori genomes has confirmed the presence of five major outer membrane proteins (OMPs) families. However, there appears to be a trend within the protein families as to which two of the three orthologs are more closely related. H. pylori 26695 and HPAG1 proteins are the most closely related more often as H. pylori J99 and HPAG1 or H. pylori J99 and 26695. Whether this is because both HPAG1 and 26695 were isolated from gastritis patients and J99 from a duodenal ulcer patient is an intriguing, but untested possibility. It has been demonstrated that several OMPs in the largest family act as adhesions, and these include BabA, SabA, OipA, AlpAB and HopZ. This unusual set of specialized OMPs may be a reflection of the adaptation of H. pylori to the unique gastric environment where it is found. Many of these genes undergo phase variation such that not all strains will produce functional proteins, and the stability of expression with passage varied with OipA > BabA > BabB > SabA. Each OMP appears to have specific functions.

Further reading: Helicobacter pylori

Microbial Biodegradation book review

2008-04-01T10:38:00.002+01:00

Interest in the microbial biodegradation of pollutants has intensified in recent years as mankind endeavors to find sustainable ways to cleanup contaminated environments. Uta Breuer (Leipzig) has written a review (Eng. Life Sci. 2008: 8, 81-82) of a recent book on this topic:

"This book is very clearly written with an abundance of information on Microbial Biodegradation from the point of view of a microbial molecular biologist. Therefore this book is strongly recommended for scientists working in the field of microbial degradation and bioremediation and certainly of general interest for environmental microbiologists. It should be made available in all libraries at universities, research institutes and industry, and is further strongly recommended to all those who are interested in life sciences."

Further information: Microbial Biodegradation: Genomics and Molecular Biology

Fungal Identification by Molecular Techniques

2008-03-31T16:58:00.002+01:00

Molecular diagnostic methods are currently being used for the early detection of many viral, bacterial, parasitic and fungal infections. Due to their high specificity and sensitivity, these methods will be inserted in the routine of the clinical laboratories to complement information provided by more conventional methods and above all, to help in the diagnosis of dubious cases. The design of specific probes, coupled to the Polymerase Chain Reaction (PCR) technique provides the required specificity and sensitivity to identify fungal species in a short time. Multicopy genes such as those of ribosomal origin are preferred by many researchers to achieve well defined results. However, because they may generate false positive results, other researchers have looked at single-copy genes of high specificity. This technology is being applied to the identification of frequently found causative agents of systemic mycoses such as Candida albicans, Aspergillus fumigatus and other species within these genera, or agents of less frequent mycoses produced by Coccidioides immitis, Cryptococcus neoformans, Histoplasma capsulatum, Paracoccidioides brasiliensis, among others.

Further reading: Pathogenic Fungi: Insights in Molecular Biology

Coronavirus book review

2008-03-25T17:11:00.003Z

from Future Virol. (2008) 3(2): 119-123.

"The book entitled Coronaviruses: Molecular and Cellular Biology presents a comprehensive review of the field of coronavirus virology. The contributors to the book are many of the experts in coronavirus virology. The contents of the book are particularly useful for those wishing to conduct research on coronaviruses because most of the authors include in their summary or conclusion paragraphs a number of key questions or problems for which research needs to be carried out to further the understanding of coronaviruses and how to treat the infections they cause. Most of the figures are very useful in helping the reader understand the narratives provided by the authors. The few tables provided are excellent in summarizing information ...

recommended for those who want to quickly be brought up to date on coronavirus research or who want to know what research questions remain to be answered in the field of coronavirus virology."

Further reading: Coronaviruses: Molecular and Cellular Biology

H. pylori book

2008-03-18T11:32:00.002Z

Helicobacter pylori is an important human pathogen that infects up to 50% of the human population. As the leading cause of peptic ulcers, gastritis and gastric cancer worldwide, the organism has been the subject of intensive research to unravel the mysteries of its genetics and cellular biology. In fact the number of publications in this field has risen dramatically in recent years making it extremely difficult for even the most diligent reader to stay abreast of progress.

A recent book on Helicobacter pylori distills the most important cutting-edge findings in the field to produce a timely and comprehensive review. Topics include: lipopolysaccharides, outer membrane proteins, motility and chemotaxis, type IV secretions systems, metal metabolism, molecular mechanisms of host adaptation, genomotyping, and proteonomics.

The book has been described as a "useful introduction to the subject for new researchers and an invaluable reference for the experienced researcher".

Further reading: Helicobacter pylori: Molecular Genetics and Cellular Biology

Spotlight on Corynebacteria

2008-03-17T17:46:00.001Z

Corynebacteria are a diverse group Gram-positive bacteria found in a range of different ecological niches such as soil, vegetables, sewage, skin, and cheese smear. Some, such as Corynebacterium diphtheriae, are important pathogens while others, such as Corynebacterium glutamicum, are of immense industrial importance. In fact C. glutamicum is one of the biotechnologically most important bacterial species in use today with an annual production of more than two million tons of amino acids, mainly L-glutamate and L-lysine. Due to its industrial importance, C. glutamicum has been studied extensively over the years, and the publication of the C. glutamicum genome sequence in 2003 provided renewed impetus to these studies. To date, the complete genome sequences of four different species have been published, and sequencing of at least two more species is ongoing. These genomic data have enabled a dramatic improvement in our understanding of the corynebacterial genome architecture, metabolic processes, species-specific traits, industrial capabilities, and potential roles in pathogenicity of humans and animals. In addition these genome sequences, allied with newly developed genetic tools will consolidate C. glutamicum as a model organism for systems biology. Research in this area has never been more exciting.

Further reading: Corynebacteria: Genomics and Molecular Biology

Rapid Diagnosis and Typing of Staphylococcus aureus

2008-03-17T16:57:00.001Z

Staphylococcus aureus is a major pathogen responsible for both nosocomial and community acquired infections. The severity of these infections varied from local benign wounds to severe systemic diseases. The situation is also complicated with emergence of bacterial resistance to common antibiotics, such as methicillin. Endemic strains of MRSA carrying multiple resistance determinants have become a worldwide nosocomial problem only in the early 1980's, carrying a threefold attributable cost and a threefold excess length of hospital stay when compared with methicillin-susceptible S. aureus bacteraemia. Recent genetic advances have enabled identification and characterization of clinical isolates in real-time. These tools support infection control strategies to limit bacterial spreading and ensure the appropriate use of diminishing antibiotics. They are also attractive for understanding the epidemiology of MRSA and the relationship between genome content and virulence.

Further reading: Francois, P. and Schrenzel, J. (2008) Rapid Diagnosis and Typing of Staphylococcus aureus In: Staphylococcus: Molecular Genetics

Rapid detection and identification of MRSA is an absolute prerequisite to adopt prompt isolation measures. Until recently, microbiological methods dedicated to MRSA identification were based on the utilization of selective growth media, which are timeconsuming and preclude same-day diagnosis. For more than one decade, nucleic acid-based identification assays have demonstrated their usefulness and robustness for the detection of hardly cultivable, non-cultivable and even killed microorganisms, as well as for the identification of specific pathogens against the background of a complex microflora. The current view is still that molecular methods are used to supplement, but not to replace cultures. MRSA molecular detection nicely illustrates this paradigm: it provides early warning but cultures are still required for further antimicrobial susceptibility testing or epidemiological typing. Molecular assays based on target nucleic acid amplification, and especially real-time PCR, have proven rapid, affordable and successful in terms of sensitivity and specificity. Current challenges for MRSA screening are centred on the selection of the most appropriate assay, both in terms of feasibility (costs, technical expertise) and assay performance. One has to be especially careful when embarking on detection strategies that are based on mobile and highly variable genetic regions, such as the SCCmec insertion site. Indeed, iterative changes in the detection protocol to adapt for emerging variants might not only affect the performance of the assay but also open unpredictable and systematic breaches in the infection control programme. To date, with several decades of hindsight, we can firmly state that molecular variations will continuously emerge, but it is currently impossible to predict where these changes will emerge. As the molecular epidemiology may substantially vary from country to country, and possibly also between different regions, this underlines the importance of having an epidemiologic molecular surveillance, ideally as close as possible to our own lab practice.

Further reading: Francois, P. and Schrenzel, J. (2008) Rapid Diagnosis and Typing of Staphylococcus aureus In: Staphylococcus: Molecular Genetics

Molecular genetics of Staphylococcus

2008-03-17T16:51:00.002Z

The staphylococci are important pathogenic bacteria responsible for a variety of diseases in humans and other animals. They are the most common cause of hospital acquired infection and antibiotic resistant strains (MRSA) have become endemic in hospitals in most countries causing major public health issues. In addition, the incidence of new strains that cause severe community-acquired infections in healthy people is increasing and MRSA strains are emerging in agricultural and domestic animals. In the race to understand staphylococcal pathogenesis the focus has been on genetics, as a bacterium can only do what its genes allow. The publication of the first staphylococcal whole genome sequence in 2001 paved the way for a greater understanding of the molecular basis of its virulence, evolution, epidemiology and drug resistance. Since then the available genomic data has mushroomed and this, coupled with the major advances in genetic know-how and the availability of better genetic tools, has allowed significant advances to be made.

Further reading: Staphylococcus: Molecular Genetics

Whole genome sequences for twelve diverse Staphylococcus aureus isolates are available and their annotation provides enormous insight into S. aureus physiology, capabilities and virulence. Whole genome microarrays, built using the sequences, have enabled whole genome regulatory responses to environmental conditions or global regulators to be investigated. Comparative genomics by sequencing and by multi-strain microarrays have identified the S. aureus population structure and how genomes vary, as well as suggesting that invasive isolates do not carry more virulence genes than carriage isolates.

A large amount of genetic information is available on several examples of this species and this, together with multilocus sequence typing (MLST) data on >1400 isolates from many countries has provided unique insights into the biology of the species and in particular, its ability to exploit a wide variety of niches. These studies show that although the great majority of S. aureus genes share a high degree of homology, virulence and antibiotic resistance genes carried on mobile genetic elements can drastically alter strain characteristics in the short-term giving the species a high degree of adaptability. These allow it to survive in many different human and animal tissues and provide the adaptability necessary to evolve resistance to new antibiotics.

Further reading: Staphylococcus: Molecular Genetics

See also: Plasmids

There is enormous variation between strains of S. aureus. Evolution occurs when genomes vary and the fittest bacteria are selected. Variation occurs in three major ways: single nucleotide polymorphisms (SNP) and other minor changes in conserved core genes; variation in hundreds of genes (particularly those encoding proteins that interact with host) that are associated with lineages of S. aureus; and acquisition and loss of mobile genetic elements (MGE) which often encode virulence and resistance genes. Barriers that block horizontal transfer of DNA, such as restriction modification, influence lineages and MGE. S. aureus MGE have their own complex life-cycles that control their spread and survival. Selection of the fittest bacteria is likely being driven by mammalian host factors and antibiotic use, and new strains of S. aureus are emerging that are increasingly virulent and resistant to antibiotics, causing novel healthcare issues.

Recommended reading: Staphylococcus: Molecular Genetics

Leishmania book

2008-03-17T16:23:00.001Z

Leishmania is a vector-borne pathogenic parasite found in 88 countries worldwide and is the causative agent of leishmaniasis. The different Leishmania species infect macrophages and dendritic cells of the host immune system, causing symptoms that range from disfiguring cutaneous and mucocutaneous lesions, widespread destruction of mucous membranes, or visceral disease affecting the haemopoetic organs. The recent publication of the complete genome sequences of three different Leishmania species provides new insights into this important pathogen and presents scientists with a vital resource to increase the understanding of Leishmania molecular and cellular biology.

A new book, Leishmania: After The Genome, has been published recently reviewing the most important aspects of current Leishmania research, providing the first coherent picture of the organism's molecular and cellular biology since the publication of the genome sequence. The book covers a range of Leishmania-specific aspects of trypanosomatid biology and pathology. Topics include: diagnosis and epidemiology, genome structure and content, regulation of gene expression, the proteome, the metabolome, differentiation, interaction with the sand fly vector, drug discovery and drug resistance.

Further reading Leishmania: After The Genome

Archaea: A new source of antibiotics?

2008-03-06T15:50:00.002Z

Peptide or protein antibiotics have been discovered in all three domains of life, and their production is nearly universal. Bacteriocin and eucaryocin research is well established, while research on archaeocins is still in its infancy. To date, only eight archaeocins (seven halocins and one sulfolobicin) have been partially or fully characterized, but hundreds of archaeocins are believed to exist, especially within the haloarchaea. The prevalence of archaeocins from other members of this domain is unknown simply because no one has looked for them. The discovery of new halocins hinges on recovery and cultivation of haloarchaeal organisms from the environment. For example, samples from a novel hypersaline field site, Wilson Hot Springs, recovered 350 halophilic organisms; preliminary analysis of 75 isolates showed that 48 were archaeal and 27 were bacterial. Significantly, 77% inhibited the growth of at least one other isolate. Inter-domain antagonisms were also present with 43 haloarchaeons inhibiting halophilic members of the domain Bacteria and 7 Bacteria antagonized haloarchaeons. Finally, archaeocin research provides excellent opportunities for discovery of novel antibiotics that may have clinical applications in addition to unique models for training students both in and outside the classroom.

More information: Archaea: New Models for Prokaryotic Biology

Heterochromatin and Gene Silencing in Yeast

2008-02-22T14:19:00.002Z

Heterochromatin is a prevalent chromatin state among eukaryotes that has critical functions in chromosome segregation, control of genomic stability and epigenetic regulation of gene expression. Recent studies (for a review see: Vavasseur et al, 2008) conducted in the fission yeast Schizosaccharomyces pombe, reveal that two RNAi complexes, the RNAi-induced transcriptional gene silencing (RITS) complex and the RNA-directed RNA polymerase complex (RDRC), are part of a RNAi machinery involved in the initiation, propagation and maintenance of heterochromatin assembly. It appears that these two complexes localize in a siRNA-dependent manner on chromosomes, at the site of heterochromatin assembly. Moreover, these studies reveal an unprecedented and central role for RNA polymerase II (RNApII) in RNAi-dependent heterochromatin assembly. RNApII synthesizes a nascent transcript that is believed to serve as a RNA platform to recruit, RITS, RDRC and possibly other complexes required for heterochromatin assembly. Recent findings indicate that RNAi as well as an exosome-dependent RNA degradation process contribute to heterochromatic gene silencing. These findings challenge the widely accepted view that heterochromatic gene silencing is caused strictly by chromatin compaction. RNAi-dependent chromatin modifications have been observed throughout the eukaryotic kingdom the mechanisms considered here may occur in a large range of eukaryotes.

Further reading:

Vavasseur et al, 2008. Heterochromatin Assembly and Transcriptional Gene Silencing under the Control of Nuclear RNAi: Lessons from Fission Yeast. In: RNA and the Regulation of Gene Expression: A Hidden Layer of Complexity. Ed, Morris K.V., Caister Academic Press, Norfolk, UK

Tost, J. 2008 Epigenetics Caister Academic Press, Norfolk, UK

Viral MicroRNAs

2008-02-20T15:36:00.002Z

MicroRNA (miRNA) is a small RNA (~22 nucleotides). The miRNA genes have been discovered in plants, invertebrates, and vertebrates. These miRNAs can regulate gene expression to inhibit translation of target messenger RNAs (mRNAs), and sometimes direct many rounds of site-specific mRNA cleavage in mammalian cells. Beyond the cutting-edged criteria of RNA interference (RNAi) by complementarily pairing of short interfering RNA (siRNA), the miRNAs, which were incomplementarily paired, are also encoded by several viruses, such as herpesviruses and human immunodeficiency virus type 1 (HIV-1). Intriguingly, gene expression of HIV-1 genome has been recently shown to be epigenetically regulated via a novel process of transcriptional repression by the miRNA of virus itself. However, role of the viral miRNA for gene regulation is not still well understood mechanistically as compared with host miRNAs.

A recently published paper (Fujii and Saksena, Chapter 7) describes the target prediction of a viral miRNA, miR-N367 and the conservation of secondary structure of pre-miR-N367 into mir-98/let-7 and mir-181a-2 in human miRNAs whose targets in HIV-1 genome could be related to HIV-1 transcriptional system. Also demonstrated is that the sequences of viral nef si/miRNA are conserved in plant miRNAs and the nef si/miRNAs was enabled to express in Arabidopsis thaliana similar to human cell. It is hypothesized that the orphaned non-selfish miRNAs may evolve and jump on to other RNAs, which can transposably lead to spread of these miRNAs from some plant and vertebrate genomes through feeding of miRNAs-containing foods, viruses, etc. Equivocally, miRNAs can be picked up into the lentiviral transposon, such as HIV-1. Therefore, the viral miR-N367 would necessarily be a HIV-1 silencer to be inclusively incorporated into HIV-1 itself. The virulence may be lost with recombination and mutation by miRNAs from the viral and host genome. The question is, whether the encoded miRNAs are mediating the viral and host genomic evolution.

Further reading:

RNA and the Regulation of Gene Expression

Epigenetics

Legionella

2008-02-15T11:58:00.000Z

More than 30 years have passed since Legionella pneumophila, the causative agent of Legionnaires' disease, was identified as a new human pathogen. First recognized due to the epidemic of pneumonia that followed the 1976 Legionnaires' convention in Philadelphia, USA, legionellosis is still a disease of medical and public interest. Legionella is commonly found in aquatic habitats, where its ability to survive and to multiply within different protozoa equips the bacterium to be transmissible and pathogenic to humans. However, these very traits also make Legionella a favoured model system to analyse the mechanisms by which bacteria survive, acquire nutrients, and replicate within macrophages and the lung.

With the application of modern molecular genetic and cell biological techniques, we have begun to understand the mechanisms used by L. pneumophila to multiply within protozoa and alveolar macrophages. Also, we have gained insight into the specific regulatory cascades that govern cell cycle-dependent differentiation as well as the general mechanisms of gene regulation in L. pneumophila.

Thanks to the recent publication of the genome sequences of four L. pneumophila strains, it is now feasible to investigate the whole genome in silico, the transcriptome via microarrays, and the proteome by two-dimensional gel electrophoresis. Thus, new questions can be asked and impressive amounts of data can be generated and evaluated. Furthermore, research in the fields of clinical features, diagnosis, treatment and epidemiology continues to generate new strategies for management and prevention of disease and more questions for basic scientists.

A newly published book on Legionella covers a wide range of topics from the history of the identification of Legionella and clinical disease treatment, to the microbe’s gene expression and secretion systems as well as its strategies for intracellular multiplication and nutrient acquisition. The book is recommended for all microbiology libraries.

Further details at Legionella: Molecular Microbiology

Symposium: Microbes and the Law

2008-02-12T11:18:00.001Z

Microbes and the Law

A course on Microbes and the Law will take place 6-7 of October, 2008 in Uppsala, Sweden. It is aimed at PhD-students in the later part of their education and junior scientists. A symposium on the same topic will be held 8-9 of October with invited speakers from all over the world.

More info from ...

Cyanobacteria Book Review

2008-02-06T09:16:00.001Z

The Cyanobacteria: Molecular Biology, Genomics and Evolution

The editors and authors of this book have succeeded admirably in producing a comprehensive, well-written book on the molecular biology, genomics and evolution of cyanobacteria. The breadth of topics covered is impressive, ranging from the crucial roles played by cyanobacteria in both the primitive and present Earth to the "nuts and bolts" of their cellular functioning. Advocates of whole genome sequences will not be disappointed, as a number of the chapters scrutinise the latest data to good effect. Whilst not strictly within the scope of the book, it is still somewhat disappointing that more information on cyanobacterial proteomics was not included to complement the genomic studies cited. However, this is a minor quibble. The greatest strength of this book is that whilst its in-depth treatment of various topics will satisfy the experienced cyanobacterial researcher, the easy to understand description of basics will also attract neophyte "cyanobacteriologists" and readers from other fields. This book deserves to become a standard reference on the molecular biology, genomics and evolution of cyanobacteria.

Review by: Dr. Roberto Anitori, Dept of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia

Full details of the book available at The Cyanobacteria: Molecular Biology, Genomics and Evolution

Conference Alert: Clostridium conference

2008-01-30T15:04:00.001Z

September 28 - October 1, 2008. 10th Clostridium Workshop (Clostridium 10)
Wageningen, The Netherlands Further information
The 10th Workshop on the Genetics and Physiology of Acid- and Solvent-producing Clostridia continues the tradition of scientific meetings that take place every two years in which scientists from all over the world come together to exchange their knowledge on these industrially interesting organisms.

Full list of microbiology conferences at Microbiology Conferences

Conference alert: Genomes 2008

2008-01-28T16:49:00.001Z

April 8 - 11, 2008. Genomes 2008 - Functional Genomics of Microorganisms
Institut Pasteur, Paris, France Further information

Microbial genomics is at the core of the scientific challenges we will have to meet in the 21st century with respect to emerging diseases, health and food science and sustainable development. Throughout the world, about 2200 genome projects are currently in progress. This impressive scientific knowledge is now further expanding as a wealth of genomics-enabled technologies in a large variety of research domains become available, ranging from sequencing and array technologies to informatics and to the analysis of host-pathogen interactions . In addition, Metagenomics and Systems B iology are expanding rapidly, promising to bring further advances. It will thus be an exciting time to bring together researchers and companies working on various aspects of the genomics field.

The emphasis of the meeting will be comparative analyses of pathogenic and environmental microbes, functional genomics, computational genomics and systems biology in the light of the new technological developments. Genomics has also dramatically changed studies concerning the interaction of microorganism s with their environment or, for pathogens, symbionts or commensals, their host. The newest results in this field will also be discussed.

For a full list of conferences please see Microbiology Conferences 2008

Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome

2008-01-25T15:56:00.002Z

A team of researchers at the J. Craig Venter Institute has created the largest man-made DNA structure by synthesizing and assembling the 582,970 base pair genome of Mycoplasma genitalium. This work, published in the journal Science (Gibson, et al, 2008) is the second of three key steps toward the goal of creating a fully synthetic organism. In the next step the team will attempt to create a living bacterial cell based entirely on the synthetically made genome.

Reference: Gibson et al (2008). Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome. Science [DOI: 10.1126/science.1151721]

Conference alert

2008-01-25T09:02:00.001Z

We would like to inform you of the following conferences.

For a full list please visit Microbiology Conferences and Meetings 2008

Any conference missing from this list? Please send details

October 19 - 23, 2008. 15th International Meeting on Frankia and Actinorhizal Plants
Bariloche, Argentina Further information: lgwall@unq.edu.ar

August 24 - September 1, 2008. Microbial Secondary Metabolites: Genomes, Signals and Communities
Inter-University Centre, Dubrovnik Further information
The Summer Schools in Applied Molecular Microbiology this year holds the Summer School on Microbial Secondary Metabolites intended for scientists at post-graduate and early post-doctoral level.

May 22 - 25, 2008. 4th International Conference on Analysis of the Microbial Cell at the Single Cell Level
Bad Schandau, Dresden, Germany Further information

August 30 - September 5, 2008. International Plasmid Biology Conference 2008
Gdansk, Poland Further information
The conference will cover all areas representing plasmids and other mobile genetic elements such as replication, partition/stability, transfer, evolution, ecology, genomics, systems biology, medical and veterinary aspects, applied aspects, and bioinformatics.

May 19 - 24, 2008. Retroviruses
Cold Spring Harbor, NY, USA Further information