Metagenomic analysis of carbohydrate-active enzymes and their contribution to marine sediment biodiversity.

Marine sediments constitute the world's most substantial long-term carbon repository. The microorganisms dwelling in these sediments mediate the transformation of fixed oceanic carbon, but their contribution to the carbon cycle is not fully understood. Previous culture-independent investigations into sedimentary microorganisms have underscored the significance of carbohydrates in the carbon cycle.

Unraveling the plasticity of translation initiation in prokaryotes: Beyond the invariant Shine-Dalgarno sequence.

Translation initiation in prokaryotes is mainly defined, although not exclusively, by the interaction between the anti-Shine-Dalgarno sequence (antiSD), located at the 3'-terminus of the 16S ribosomal RNA, and a complementary sequence, the ribosome binding site, or Shine-Dalgarno (SD), located upstream of the start codon in prokaryotic mRNAs. The antiSD has a conserved 5'-CCUCC-3' core, but inter-species variations have been found regarding the participation of flanking bases in binding. These variations have been described for certain bacteria and, to a lesser extent, for some archaea.

Correction: Whole genome variation in 27 Mexican indigenous populations, demographic and biomedical insights.

[This corrects the article DOI: 10.1371/journal.pone.

Whole genome variation in 27 Mexican indigenous populations, demographic and biomedical insights.

There has been limited study of Native American whole genome diversity to date, which impairs effective implementation of personalized medicine and a detailed description of its demographic history. Here we report high coverage whole genome sequencing of 76 unrelated individuals, from 27 indigenous groups across Mexico, with more than 97% average Native American ancestry. On average, each individual has 3.

The canonical RdDM pathway mediates the control of seed germination timing under salinity.

Plants respond to adverse environmental cues by adjusting a wide variety of processes through highly regulated mechanisms to maintain plant homeostasis for survival. As a result of the sessile nature of plants, their response, adjustment and adaptation to the changing environment is intimately coordinated with their developmental programs through the crosstalk of regulatory networks. Germination is a critical process in the plant life cycle, and thus plants have evolved various strategies to control the timing of germination according to their local environment.

Demographic history and biologically relevant genetic variation of Native Mexicans inferred from whole-genome sequencing.

Understanding the genetic structure of Native American populations is important to clarify their diversity, demographic history, and to identify genetic factors relevant for biomedical traits. Here, we show a demographic history reconstruction from 12 Native American whole genomes belonging to six distinct ethnic groups representing the three main described genetic clusters of Mexico (Northern, Southern, and Maya). Effective population size estimates of all Native American groups remained below 2,000 individuals for up to 10,000 years ago.

The genomes of four tapeworm species reveal adaptations to parasitism.

Tapeworms (Cestoda) cause neglected diseases that can be fatal and are difficult to treat, owing to inefficient drugs. Here we present an analysis of tapeworm genome sequences using the human-infective species Echinococcus multilocularis, E. granulosus, Taenia solium and the laboratory model Hymenolepis microstoma as examples.

Functional analysis of the group 4 late embryogenesis abundant proteins reveals their relevance in the adaptive response during water deficit in Arabidopsis.

Late-Embryogenesis Abundant (LEA) proteins accumulate to high levels during the last stages of seed development, when desiccation tolerance is acquired, and in vegetative and reproductive tissues under water deficit, leading to the hypothesis that these proteins play a role in the adaptation of plants to this stress condition. In this work, we obtained the accumulation patterns of the Arabidopsis (Arabidopsis thaliana) group 4 LEA proteins during different developmental stages and plant organs in response to water deficit. We demonstrate that overexpression of a representative member of this group of proteins confers tolerance to severe drought in Arabidopsis plants.

The global intrinsic curvature of archaeal and eubacterial genomes is mostly contained in their dinucleotide composition and is probably not an adaptation.

Until now, the genomic DNA of all eubacteria analyzed has been hyper-curved, its global intrinsic curvature being higher than that of a random sequence. In contrast, that rule failed for archaea or eukaryotes, which could be either hypo- or hyper-curved. The existence of the rule suggested that, at least for eubacteria, global intrinsic curvature is adaptive.

Highly hydrophilic proteins in prokaryotes and eukaryotes are common during conditions of water deficit.

The late embryogenesis abundant (LEA) proteins are plant proteins that are synthesized at the onset of desiccation in maturing seeds and in vegetative organs exposed to water deficit. Here, we show that most LEA proteins are comprised in a more widespread group, which we call "hydrophilins." The defining characteristics of hydrophilins are high glycine content (>6%) and a high hydrophilicity index (>1.

Characterization of Phaseolus vulgaris cDNA clones responsive to water deficit: identification of a novel late embryogenesis abundant-like protein.

Six cDNA clones from Phaseolus vulgaris, whose expression is induced by water deficit and ABA treatment (rsP cDNAs) were identified and characterized. The sequence analyses of the isolated clones suggest that they encode two types of late-embryogenesis abundant (LEA) proteins, a class-1 cytoplasmic low-molecular-weight heat shock protein (lmw-HSP), a lipid transfer protein (LTP), and two different proline-rich proteins (PRP). One of the putative LEA proteins identified corresponds to a novel 9.

Abscisic acid inhibits germination of mature Arabidopsis seeds by limiting the availability of energy and nutrients.

The addition of abscisic acid (ABA) to mature non-dormant seeds inhibits their germination. This effect of ABA might be related to its natural function as an endogenous inhibitor of precocious germination during seed formation. In this work, we studied how ABA affects the germination of mature seeds and the growth of nascent seedlings of Arabidopsis thaliana (L.

Cell-Wall Proteins Induced by Water Deficit in Bean (Phaseolus vulgaris L.) Seedlings.

In the last few years, much attention has been given to the role of proteins that accumulate during water deficit. In this work, we analyzed the electrophoretic patterns of basic protein extracts, enriched for a number of cell-wall proteins, from bean (Phaseolus vulgaris L.) seedlings and 21-d-old plants subjected to water deficit.

Promoter selection by a bacterial enhancer-like activator element (BELE) in Escherichia coli.

The Escherichia coli glnA gene promoter glnAp2 is activated by an element able to act bidirectionally and at variable distance over the DNA. We demonstrate here that this activating element does not influence another promoter, 82p, adjacent to it, from which a gene is transcribed in opposite direction to glnA. Thus, although it displays a great flexibility, this element can activate selectively.

Glutamine synthetase-constitutive mutation affecting the glnALG upstream promoter of Escherichia coli.

The spontaneous gln-76 mutation of Escherichia coli (Osorio et al., Mol. Gen.

Nucleotide sequence of the glnA-glnL intercistronic region of Escherichia coli.

The nucleotide (nt) sequence of a 682-bp fragment containing the 3' end of the glnA gene, the region between the glnA and glnL genes, and the 5' end of the glnL gene from Escherichia coli was determined. This segment contains the region coding for the last 107 amino acids (aa) of glutamine synthetase, including the adenylylation site of this enzyme. The analysis of this sequence revealed two REP sequences, a Rho-independent terminator, the putative glnL promoter and the possible binding site for the glnG product, NRI.

Structural organization of the genes that encode two glutamate synthase subunits of Escherichia coli.

Plasmid pRSP20, a recombinant plasmid isolated from the Clarke-Carbon Escherichia coli gene bank, contains the two genes coding for the subunits of glutamate synthase (GOGAT). We have constructed several derivatives of pRSP20, and analyzed the direction of transcription and genetic organization of these genes. Unexpectedly, we have found that although they are tightly linked and are transcribed in the same direction, each of them has its own promoter.