Catálogo de publicaciones - revistas

<jats:title>Abstract</jats:title><jats:p>Microorganisms play a central role in biotechnology and it is key that we develop strategies to engineer and optimize their functionality. To this end, most efforts have focused on introducing genetic manipulations in microorganisms which are then grown either in monoculture or in mixed‐species consortia. An alternative strategy to optimize microbial processes is to rationally engineer the environment in which microbes grow. The microbial environment is multidimensional, including factors such as temperature, pH, salinity, nutrient composition, etc. These environmental factors all influence the growth and phenotypes of microorganisms and they generally “interact” with one another, combining their effects in complex, non‐additive ways. In this piece, we overview the origins and consequences of these “interactions” between environmental factors and discuss how they have been built into statistical, bottom‐up predictive models of microbial function to identify optimal environmental conditions for monocultures and microbial consortia. We also overview alternative “top‐down” approaches, such as genetic algorithms, to finding optimal combinations of environmental factors. By providing a brief summary of the state of this field, we hope to stimulate further work on the rational manipulation and optimization of the microbial environment.</jats:p>

<jats:title>Abstract</jats:title><jats:p>The site‐specific recombination pathway of bacteriophage λ encompasses isoenergetic but highly directional and tightly regulated integrative and excisive reactions that integrate and excise the vial chromosome into and out of the bacterial chromosome. The reactions require 240 bp of phage DNA and 21 bp of bacterial DNA comprising 16 protein binding sites that are differentially used in each pathway by the phage‐encoded Int and Xis proteins and the host‐encoded integration host factor and factor for inversion stimulation proteins. Structures of higher‐order protein–DNA complexes of the four‐way Holliday junction recombination intermediates provided clarifying insights into the mechanisms, directionality, and regulation of these two pathways, which are tightly linked to the physiology of the bacterial host cell. Here we review our current understanding of the mechanisms responsible for regulating and executing λ site‐specific recombination, with an emphasis on key studies completed over the last decade.</jats:p>

<jats:title>Abstract</jats:title><jats:p>The sole unifying feature of the incredibly diverse Archaea is their isoprenoid‐based ether‐linked lipid membranes. Unique lipid membrane composition, including an abundance of membrane‐spanning tetraether lipids, impart resistance to extreme conditions. Many questions remain, however, regarding the synthesis and modification of tetraether lipids and how dynamic changes to archaeal lipid membrane composition support hyperthermophily. Tetraether membranes, termed glycerol dibiphytanyl glycerol tetraethers (GDGTs), are generated by tetraether synthase (Tes) by joining the tails of two bilayer lipids known as archaeol. GDGTs are often further specialized through the addition of cyclopentane rings by GDGT ring synthase (Grs). A positive correlation between relative GDGT abundance and entry into stationary phase growth has been observed, but the physiological impact of inhibiting GDGT synthesis has not previously been reported. Here, we demonstrate that the model hyperthermophile <jats:italic>Thermococcus kodakarensis</jats:italic> remains viable when Tes (TK2145) or Grs (TK0167) are deleted, permitting phenotypic and lipid analyses at different temperatures. The absence of cyclopentane rings in GDGTs does not impact growth in <jats:italic>T. kodakarensis</jats:italic>, but an overabundance of rings due to ectopic Grs expression is highly fitness negative at supra‐optimal temperatures. In contrast, deletion of Tes resulted in the loss of all GDGTs, cyclization of archaeol, and loss of viability upon transition to the stationary phase in this model archaea. These results demonstrate the critical roles of highly specialized, dynamic, isoprenoid‐based lipid membranes for archaeal survival at high temperatures.</jats:p>

<jats:title>Abstract</jats:title><jats:p>The flagellar motor is a powerful macromolecular machine used to propel bacteria through various environments. We determined that flagellar motility of the alpha‐proteobacterium <jats:italic>Sinorhizobium meliloti</jats:italic> is nearly abolished in the absence of the transcriptional regulator LdtR, known to influence peptidoglycan remodeling and stress response. LdtR does not regulate motility gene transcription. Remarkably, the motility defects of the Δ<jats:italic>ldtR</jats:italic> mutant can be restored by secondary mutations in the motility gene <jats:italic>motA</jats:italic> or a previously uncharacterized gene in the flagellar regulon, which we named <jats:italic>motS</jats:italic>. MotS is not essential for <jats:italic>S. meliloti</jats:italic> motility and may serve an accessory role in flagellar motor function. Structural modeling predicts that MotS comprised an N‐terminal transmembrane segment, a long‐disordered region, and a conserved β‐sandwich domain. The C terminus of MotS is localized in the periplasm. Genetics based substitution of MotA with MotA<jats:sub>G12S</jats:sub> also restored the Δ<jats:italic>ldtR</jats:italic> motility defect. The MotA<jats:sub>G12S</jats:sub> variant protein features a local polarity shift at the periphery of the MotAB stator units. We propose that MotS may be required for optimal alignment of stators in wild‐type flagellar motors but becomes detrimental in cells with altered peptidoglycan. Similarly, the polarity shift in stator units composed of MotB/MotA<jats:sub>G12S</jats:sub> might stabilize its interaction with altered peptidoglycan.</jats:p>

<jats:title>Abstract</jats:title><jats:p>Increasing evidence suggests that DNA phosphorothioate (PT) modification serves several purposes in the bacterial host, and some restriction enzymes specifically target PT‐DNA. PT‐dependent restriction enzymes (PDREs) bind PT‐DNA through their DNA sulfur binding domain (SBD) with dissociation constants (<jats:italic>K</jats:italic><jats:sub>D</jats:sub>) of 5 nM~1 μM. Here, we report that SprMcrA, a PDRE, failed to dissociate from PT‐DNA after cleavage due to high binding affinity, resulting in low DNA cleavage efficiency. Expression of SBDs in <jats:italic>Escherichia coli</jats:italic> cells with PT modification induced a drastic loss of cell viability at 25°C when both DNA strands of a PT site were bound, with one SBD on each DNA strand. However, at this temperature, SBD binding to only one PT DNA strand elicited a severe growth lag rather than lethality. This cell growth inhibition phenotype was alleviated by raising the growth temperature. An in vitro assay mimicking DNA replication and RNA transcription demonstrated that the bound SBD hindered the synthesis of new DNA and RNA when using PT‐DNA as the template. Our findings suggest that DNA modification‐targeting proteins might regulate cellular processes involved in DNA metabolism in addition to being components of restriction‐modification systems and epigenetic readers.</jats:p>

<jats:title>Abstract</jats:title><jats:p>YbeX of <jats:italic>Escherichia coli</jats:italic>, a member of the CorC protein family, is encoded in the same operon with ribosome‐associated proteins YbeY and YbeZ. Here, we report the involvement of YbeX in ribosomal metabolism. The <jats:italic>ΔybeX</jats:italic> cells accumulate distinct 16S rRNA degradation intermediates in the 30S particles and the 70S ribosomes. <jats:italic>E. coli</jats:italic> lacking <jats:italic>ybeX</jats:italic> has a lengthened lag phase upon outgrowth from the stationary phase. This growth phenotype is heterogeneous at the individual cell level and especially prominent under low extracellular magnesium levels. The <jats:italic>ΔybeX</jats:italic> strain is sensitive to elevated growth temperatures and to several ribosome‐targeting antibiotics that have in common the ability to induce the cold shock response in <jats:italic>E. coli</jats:italic>. Although generally milder, the phenotypes of the <jats:italic>ΔybeX</jats:italic> mutant overlap with those caused by <jats:italic>ybeY</jats:italic> deletion. A genetic screen revealed partial compensation of the <jats:italic>ΔybeX</jats:italic> growth phenotype by the overexpression of YbeY. These findings indicate an interconnectedness among the <jats:italic>ybeZYX</jats:italic> operon genes, highlighting their roles in ribosomal assembly and/or degradation.</jats:p>

<jats:title>Abstract</jats:title><jats:p>Bacterial genomes are folded and organized into compact yet dynamic structures, called nucleoids. Nucleoid orchestration involves many factors at multiple length scales, such as nucleoid‐associated proteins and liquid–liquid phase separation, and has to be compatible with replication and transcription. Possibly, genome organization plays an intrinsic role in transcription regulation, in addition to classical transcription factors. In this review, we provide arguments supporting this view using the Gram‐positive bacterium <jats:italic>Bacillus subtilis</jats:italic> as a model. Proteins BsSMC, HBsu and Rok all impact the structure of the <jats:italic>B. subtilis</jats:italic> chromosome. Particularly for Rok, there is compelling evidence that it combines its structural function with a role as global gene regulator. Many studies describe either function of Rok, but rarely both are addressed at the same time. Here, we review both sides of the coin and integrate them into one model. Rok forms unusually stable DNA–DNA bridges and this ability likely underlies its repressive effect on transcription by either preventing RNA polymerase from binding to DNA or trapping it inside DNA loops. Partner proteins are needed to change or relieve Rok‐mediated gene repression. Lastly, we investigate which features characterize H‐NS‐like proteins, a family that, at present, lacks a clear definition.</jats:p>

<jats:title>Abstract</jats:title><jats:p>Gene transfer agents (GTAs) are genetic elements derived from ancestral bacteriophages that have become domesticated by the host. GTAs are present in diverse prokaryotic organisms, where they can facilitate horizontal gene transfer under certain conditions. Unlike typical bacteriophages, GTAs do not exhibit any preference for the replication or transfer of the genes encoding them; instead, they exhibit a remarkable capacity to package chromosomal, and sometimes extrachromosomal, DNA into virus‐like capsids and disseminate it to neighboring cells. Because GTAs resemble defective prophages, identification of novel GTAs is not trivial. The detection of candidates relies on the genetic similarity to known GTAs, which has been fruitful in α‐proteobacterial lineages but challenging in more distant bacteria. Here we consider several fundamental questions: What is the true prevalence of GTAs in prokaryote genomes? Given there are high costs for GTA production, what advantage do GTAs provide to the bacterial host to justify their maintenance? How is the bacterial chromosome recognized and processed for inclusion in GTA particles? This article highlights the challenges in comprehensively understanding GTAs' prevalence, function and DNA packaging method. Going forward, broad study of atypical GTAs and use of ecologically relevant conditions are required to uncover their true impact on bacterial chromosome evolution.</jats:p>