Biochemical genetics

The field under review is growing so rapidly that it is impossible to cover more than a sampling of recent papers in the allotted space. Important subjects such as the genetics and chemistry of viruses and certain topics in bacterial genetics have had to be omitted, while others have not received the treatment they deserve. Studies of a primarily biochemical nature in which mutants have been employed as tools have been reviewed, as is customary, although it is recognized that their genetic interest lies chiefly in their providing materials for the further study of gene action

Full-genome sequence of the plant growth-promoting bacterium Pseudomonas protegens CHA0.

We report the complete genome sequence of the free-living bacterium Pseudomonas protegens (formerly Pseudomonas fluorescens) CHA0, a model organism used in plant-microbe interactions, biological control of phytopathogens, and bacterial genetics

Influential cited references in FEMS Microbiology Letters: lessons from Reference Publication Year Spectroscopy (RPYS)

The journal FEMS Microbiology Letters covers all aspects of microbiology including virology. On which scientific shoulders do the papers published in this journal stand? Which are the classic papers used by the authors? We aim to answer these questions in this study by applying the Reference Publication Year Spectroscopy (RPYS) analysis to all papers published in this journal between 1977 and 2017. In total, 16 837 publications with 410 586 cited references are analyzed. Mainly, the studies published in the journal FEMS Microbiology Letters draw knowledge from methods developed to quantify or characterize biochemical substances such as proteins, nucleic acids, lipids, or carbohydrates and from improvements of techniques suitable for studies of bacterial genetics. The techniques frequently used for studying the genetic of microorganisms in FEMS Microbiology Letters' studies were developed using samples prepared from microorganisms. Methods required for the investigation of proteins, carbohydrates, or lipids were mostly transferred from other fields of life science to microbiology

Physiological Aspects of Genetics

The biological sciences appear to be in the midst of a period of unprecedented progress. An important salient in the advance is the general recognition of the significance of genes in the economy of the organism. The change is largely one in point of view. Many biologists have for a long time appreciated the basic nature of the gene and its role in development and function, but these relatively enlightened individuals have for the most part belonged to a small group of specialists that has tended to remain in isolation. The restraining fences are now being broken down with gratifying rapidity. Biochemists have begun to think in terms of genes because it has been demonstrated to them not only that the chemical reactions which make up living systems are under the fairly immediate supervision of these units of inheritance, but also that genetics provides a powerful tool with which a great deal can be learned about metabolic systems. In bacteriology, too, one sees the effects of an altered point of view toward genetics. Only a few years ago a bacteriologist who so much as raised the question of the existence of genes in bacteria was regarded as a renegade and heretic by his more orthodox fellowmen. It has now become acceptable to speak of bacterial genes; in fact, a recognized field of bacterial genetics has grown up almost over night (l)

Comparative genome analysis identifies few traits unique to the Escherichia coli ST131 H30Rx clade and extensive mosaicism at the capsule locus

Background: E.coli ST131 is a globally disseminated clone of multi-drug resistant E. coli responsible for that vast majority of global extra-intestinal E. coli infections. Recent global genomic epidemiological studies have highlighted the highly clonal nature of this group of bacteria, however there appears to be inconsistency in some phenotypes associated with the clone, in particular capsule types as determined by K-antigen testing both biochemically and by PCR. Results: We performed improved quality assemblies on ten ST131 genomes previously sequenced by our group and compared them to a new reference genome sequence JJ1886 to identify the capsule loci across the drug-resistant clone H30Rx. Our data shows considerable genetic diversity within the capsule locus of H30Rx clone strains which is mirrored by classical K antigen testing. The varying capsule locus types appear to be randomly distributed across the H30Rx phylogeny suggesting multiple recombination events at this locus, but that this capsule heterogeneity has little to no effect on virulence associated phenotypes in vitro. Conclusions: Our data provides a framework for determining the capsular genetics of E. coli ST131 and further beyond to ExPEC strains, and highlights how capsular mosaicism may be an important strategy in becoming a successful globally disseminated human pathogen

Bacteria are not Lamarckian

Instructive influence of environment on heredity has been a debated topic for centuries. Darwin's identification of natural selection coupled to chance variation as the driving force for evolution, against a formal interpretation proposed by Lamarck, convinced most scientists that environment does not specifically instruct evolution in an oriented direction. This is true for multicellular organisms. In contrast, bacteria were long thought of as prone to receive oriented influences from their environment, although much was in favour of the Darwinian route (1). In this context Cairns et al. raised a passionate debate by suggesting that bacteria generate mutations oriented by the environmental conditions (2). Several independent pieces of work subsequently demonstrated that mutations overcoming specific defects arised as a consequence of cultivation on specific media (3-7). Two diametrically opposed interpretations were proposed to explain these observations : either induction of mutations instructed by the environment (e.g. by a process involving a putative reverse transcription) or selection of variants among a large set of mutant bacteria generated when stress conditions are present. The experiments presented below indicate that the Darwinian paradigm is the most plausible.Comment: Work performed to show that the interpretation of Cairns experiments on adaptive mutations was wrong: bacteria are not lamarckian; the set up provided shows that when submitted to some sort of starvation, individual within colonies can find unexpected ways ou

The Chlamydomonas genome project: A decade on

The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis, and micronutrient homeostasis. Ten years since its genome project was initiated an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the omics era. Housed at Phytozome, the plant genomics portal of the Joint Genome Institute (JGI), the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of whole transcriptome sequencing (RNA-Seq) data. We present here the past, present, and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions, and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes

Salmonella Typhimurium interferes with the humoral immune response in pigs

Foodborne salmonellosis is one of the most important bacterial zoonotic diseases worldwide. Salmonella Typhimurium is the serovar most frequently isolated from slaughter pigs in Europe. Circumvention of the host’s immune system by Salmonella might contribute to persistent infection of pigs. We found that Salmonella Typhimurium strain 112910a, which is able to persist in pigs, was capable of downregulating the expression of major histocompatibility class II (MHC II) molecules on porcine alveolar macrophages (PAM) in a Salmonella pathogenicity island 2 (SPI-2) dependent way and that MHC II downregulation was Salmonella strain dependent. The MHC II downregulation capacity was abolished when bacteria were opsonized with Salmonella-specific antibodies. Furthermore, intracellular proliferation of Salmonella Typhimurium opsonized with Salmonella positive pig serum was significantly impaired compared to that of the bacteria opsonized with negative pig serum. In a subsequent in vivo experiment, Salmonella Typhimurium strain MB2216 that did not induce MHC II downregulation in vitro, was shed less and persisted less but induced earlier seroconversion in pigs than strain 112910a. From the in vitro data, it is proposed that Salmonella Typhimurium downregulates the humoral immune response to promote intracellular survival inside porcine macrophages, contributing to long-term Salmonella persistence in pigs. The fact that the less persistent strain MB2216 induced earlier seroconversion than strain 112910a is of major interest for Salmonella-monitoring programs primarily based on serology, since this indicates that more persisting strains are more likely to escape serological detection