Towards in vivo regulon kinetics: PurR activation by 5-phosphoribosyl-α-1-pyrophosphate during purine depletion in Lactococcus lactis

Riboswitch RSthiT as a molecular tool in Lactococcus lactis

Previous RNA sequencing has allowed the identification of 129 long 5′ untranslated regions (UTRs) in the Lactococcus lactis MG1363 transcriptome. These sequences potentially harbor cis-acting riboswitches. One of the identified extended 5′ UTRs is a putative thiamine pyrophosphate (TPP) riboswitch. It is located immediately upstream of the thiamine transporter gene thiT (llmg_0334). To confirm this assumption, the 5′-UTR sequence was placed upstream of the gene encoding the superfolder green fluorescent protein (sfGFP), sfgfp, allowing the examination of the expression of sfGFP in the presence or absence of thiamine in the medium. The results show that this sequence indeed represents a thiamine-responsive TPP riboswitch. This RNA-based genetic control device was used to successfully restore the mutant phenotype of an L. lactis strain lacking the major autolysin gene, acmA. The L. lactisthiT TPP riboswitch (RS_thiT) is a useful molecular genetic tool enabling the gradual downregulation of the expression of genes under its control by adjusting the thiamine concentration.

IMPORTANCE The capacity of microbes with biotechnological importance to adapt to and survive under quickly changing industrial conditions depends on their ability to adequately control gene expression. Riboswitches are important RNA-based elements involved in rapid and precise gene regulation. Here, we present the identification of a natural thiamine-responsive riboswitch of Lactococcus lactis, a bacterium used worldwide in the production of dairy products. We used it to restore a genetic defect in an L. lactis mutant and show that it is a valuable addition to the ever-expanding L. lactis genetic toolbox.

Metabolic control of virulence factor production in Staphylococcus aureus

As investigators decipher the underlining mechanisms of Staphylococcus aureus pathogenesis, it is becoming apparent that perturbations in central metabolism alter virulence factor production and infection outcomes. It is also evident that S. aureus has the ability to metabolically adapt to improve colonization and overcome challenges imparted by the immune system. Altered metabolite pools modify virulence factor production suggesting that proper functioning of a core metabolic network is necessary for successful niche colonization and pathogenesis. Herein we discuss four examples of transcriptional regulators that monitor metabolic status. These regulatory systems sense perturbations in the metabolic network and respond by altering the transcription of genes utilized for central metabolism, energy generation and pathogenesis.

Genetics of Lactococci

Lactococcus lactis is the best characterized species among the lactococci, and among the most consumed food-fermenting bacteria worldwide. Thanks to their importance in industrialized food production, lactococci are among the lead bacteria understood for fundamental metabolic pathways that dictate growth and survival properties. Interestingly, lactococci belong to the Streptococcaceae family, which includes food, commensal and virulent species. As basic metabolic pathways (e.g., respiration, metal homeostasis, nucleotide metabolism) are now understood to underlie virulence, processes elucidated in lactococci could be important for understanding pathogen fitness and synergy between bacteria. This chapter highlights major findings in lactococci and related bacteria, and covers five themes: distinguishing features of lactococci, metabolic capacities including the less known respiration metabolism in Streptococcaceae, factors and pathways modulating stress response and fitness, interbacterial dialogue via metabolites, and novel applications in health and biotechnology.

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

Phosphoribosyl diphosphate (PRPP) is an important intermediate in cellular metabolism. PRPP is synthesized by PRPP synthase, as follows: ribose 5-phosphate + ATP → PRPP + AMP. PRPP is ubiquitously found in living organisms and is used in substitution reactions with the formation of glycosidic bonds. PRPP is utilized in the biosynthesis of purine and pyrimidine nucleotides, the amino acids histidine and tryptophan, the cofactors NAD and tetrahydromethanopterin, arabinosyl monophosphodecaprenol, and certain aminoglycoside antibiotics. The participation of PRPP in each of these metabolic pathways is reviewed. Central to the metabolism of PRPP is PRPP synthase, which has been studied from all kingdoms of life by classical mechanistic procedures. The results of these analyses are unified with recent progress in molecular enzymology and the elucidation of the three-dimensional structures of PRPP synthases from eubacteria, archaea, and humans. The structures and mechanisms of catalysis of the five diphosphoryltransferases are compared, as are those of selected enzymes of diphosphoryl transfer, phosphoryl transfer, and nucleotidyl transfer reactions. PRPP is used as a substrate by a large number phosphoribosyltransferases. The protein structures and reaction mechanisms of these phosphoribosyltransferases vary and demonstrate the versatility of PRPP as an intermediate in cellular physiology. PRPP synthases appear to have originated from a phosphoribosyltransferase during evolution, as demonstrated by phylogenetic analysis. PRPP, furthermore, is an effector molecule of purine and pyrimidine nucleotide biosynthesis, either by binding to PurR or PyrR regulatory proteins or as an allosteric activator of carbamoylphosphate synthetase. Genetic analyses have disclosed a number of mutants altered in the PRPP synthase-specifying genes in humans as well as bacterial species.

Ribosomal dimerization factor YfiA is the major protein synthesized after abrupt glucose depletion in Lactococcus lactis

We analysed the response of the model bacterium Lactococcus lactis to abrupt depletion of glucose after several generations of exponential growth. Glucose depletion resulted in a drastic drop in the energy charge accompanied by an extremely low GTP level and an almost total arrest of protein synthesis. Strikingly, the cell prioritized the continued synthesis of a few proteins, of which the ribosomal dimerization factor YfiA was the most highly expressed. Transcriptome analysis showed no immediate decrease in total mRNA levels despite the lowered nucleotide pools and only marginally increased levels of the yfiA transcript. Severe up-regulation of genes in the FruR, CcpA, ArgR and AhrC regulons were consistent with a downshift in carbon and energy source. Based upon the results, we suggest that transcription proceeded long enough to record the transcriptome changes from activation of the FruR, CcpA, ArgR and AhrC regulons, while protein synthesis stopped due to an extremely low GTP concentration emerging a few minutes after glucose depletion. The yfiA deletion mutant exhibited a longer lag phase upon replenishment of glucose and a faster death rate after prolonged starvation supporting that YfiA-mediated ribosomal dimerization is important for keeping long-term starved cells viable and competent for growth initiation.

Naturalizing semiotics: The triadic sign of Charles Sanders Peirce as a systems property

The father of pragmatism, Charles Sanders Peirce, gave in 1903 the following definition of a sign: "A Sign, or Representamen, is a First which stands in such a genuine triadic relation to a Second, called its Object, as to be capable of determining a Third, called its Interpretant, to assume the same triadic relation to its Object in which it stands itself to the same Object. The triadic relation is genuine, that is its three members are bound together by it in a way that does not consist in any complexus of dyadic relations". Despite its cult status and its pragmatic foundation, the Peircean sign has never revealed its true potential by being integrated into a formal system. In the present report, a reconstruction of the sign model is presented, which may at first appear somewhat obvious and superficial. However by use of the reconstructed model, the above statement and the majority of Peirce's other statements about the nature of signs fall into place. Instead of defining three links between Object (O), Representamen (R), and Interpretant (I), the sign is described as having a single three-dimensional link, specifying its location in a three dimensional (O,R,I) linkage space. To understand and explain sign function, the process of sign utilization (semiosis) has to be divided into two temporally separated phases, a sign-establishment phase where a three-dimensional link (Ψ(O,R,I)) is formed between three sign elements, and a later sign-interpretation phase where the established linkage is used for inferring significance to a novel phenomenon, if this satisfies the criteria for being a Representamen for the sign. Numerous statements from Peirce indicate that he used a two-staged semiosis paradigm although he did not state that explicitly. The three-dimensional model was primarily constructed for use in biosemiotics, as an exploratory frame for mapping the evolutionary establishment of sign links, which logically must have preceded the fixation of any regulatory process in molecular biological systems. It became clear, however, that the model is able to clarify many of the difficult explanations offered by Peirce about his sign model. I make no claim that Peirce used a similar type of three-dimensional model, because he explicitly used the chemical atom as naturalization (natural scientific explanation) for his sign model, an interesting but problematic analogy. In order to discuss common versus specific semiotic scaffolds for molecular biosemiotics, biosemiotics and semiotics proper, I start with a generic definition of the three-dimensional sign system, using human semiosis as examples. After this, the major part of the paper, I define the specific biochemical and evolutionary scaffolds that is used for obtaining the evolutionary memory that is needed for sign establishment. To exemplify semiosis according to the present model I present a typical situation where a Representamen (RE) and an object (OE) in the establishment phase are frequently encountered together by a sign interpreter. The process that links specific Representamens to specific Objects will first involve the recognition of the specific traits that distinguish the two sign elements. Subsequently the establishment process leads to the creation of a specific systems-state, called the Interpretant, which links the two traits in a way that allows retrieval of the information (a memory function). During a later interpretation phase, a hypothetical Object will be inferred by the interpreter when a Representamen (RI) harboring the required characteristics is encountered. This inference happens through a memory retrieval process, irrespective of the fact that relevant Objects of the sign may never be encountered after establishment. A simplified scheme for computer neural network algorithms is introduced as an example of such a system. Since the Peircean sign according to this definition is a systems property, there can be no sign without a sign interpreting systems or without some kind of memory function. A sign interpreter will thus harbor a semiotic scaffold that consists of at least an input sensor and an interpreting system coupled to a memory function. Further border conditions for semiotic scaffolds will be introduced. Peirce published a comprehensive sign definition system, but he allowed only ten sign classes, selected from the twenty-seven sign classes that result from his three main subdivisions, each containing three classes. His allowed sign classes are here identified as those which do not infer more significance during interpretation than was warranted during establishment. The excluded sign classes are either undefinable in his system or are of such a nature that the objects during interpretation are inferred to be much more significant than what was warranted during establishment. Occult signs are of these forbidden free-wheeling types, and it is postulated that they were omitted because Peirce defined his sign classes for use in a novel sign based logical system, where such over-signification would be detrimental.

Multi-stress resistance in Lactococcus lactis is actually escape from purine-induced stress sensitivity

Multi-stress resistance is a widely documented and fascinating phenotype of lactococci where single mutations, preferentially in genes involved in nucleotide metabolism and phosphate uptake, result in elevated tolerance to multiple stresses simultaneously. In this report, we have analysed the metabolic basis behind this multi-stress-resistance phenotype in Lactococcus lactis subsp. cremoris MG1363 using acid stress as a model of multi-stress resistance. Surprisingly, we found that L. lactis MG1363 is fully resistant to pH 3.0 in the chemically defined SA medium, contrary to its sensitivity in the rich and complex M17 medium. When salvage of purines and subsequent conversion to GTP was permitted in various genetic backgrounds of L. lactis MG1363, the cells became sensitive to acid stress, indicating that an excess of guanine nucleotides induces stress sensitivity. The addition of phosphate to the acid-stress medium increased the stress sensitivity of L. lactis MG1363. It is also shown that high intracellular guanine nucleotide pools confer increased sensitivity to high temperatures, thus showing that it is indeed a multi-stress phenotype. Our analysis suggests that an increased level of guanine nucleotides is formed as a result of an improved conversion of guanosine in the salvage pathway. Based upon our findings, we suggest that L. lactis MG1363 is naturally multi-stress resistant in habitats devoid of any purine source. However, any exogenous purine that results in increased guanine nucleotide pools renders the bacterium sensitive to environmental stresses.