scholarly journals Comparative Genomics of Leuconostoc carnosum

2021 ◽  
Vol 11 ◽  
Author(s):  
Francesco Candeliere ◽  
Stefano Raimondi ◽  
Gloria Spampinato ◽  
Moon Yue Feng Tay ◽  
Alberto Amaretti ◽  
...  
Keyword(s):  
Amino Acids ◽  
Core Genome ◽  
Meat Products ◽  
Genome Comparison ◽  
The Core ◽  
Functional Potential ◽  
Pathway Reconstruction ◽  
Genes Encoding ◽  
Food Matrices ◽  
Leuconostoc Carnosum

Leuconostoc carnosum is a known colonizer of meat-related food matrices. It reaches remarkably high loads during the shelf life in packaged meat products and plays a role in spoilage, although preservative effects have been proposed for some strains. In this study, the draft genomes of 17 strains of L. carnosum (i.e., all the strains that have been sequenced so far) were compared to decipher their metabolic and functional potential and to determine their role in food transformations. Genome comparison and pathway reconstruction indicated that L. carnosum is a compact group of closely related heterofermentative bacteria sharing most of the metabolic features. Adaptation to a nitrogen-rich environment, such as meat, is evidenced by 23 peptidase genes identified in the core genome and by the autotrophy for nitrogen compounds including several amino acids, vitamins, and cofactors. Genes encoding the decarboxylases yielding biogenic amines were not present. All the strains harbored 1–4 of 32 different plasmids, bearing functions associated to proteins hydrolysis, transport of amino acids and oligopeptides, exopolysaccharides, and various resistances (e.g., to environmental stresses, bacteriophages, and heavy metals). Functions associated to bacteriocin synthesis, secretion, and immunity were also found in plasmids. While genes for lactococcin were found in most plasmids, only three harbored the genes for leucocin B, a class IIa antilisterial bacteriocin. Determinants of antibiotic resistances were absent in both plasmids and chromosomes.

scholarly journals Phenotypic Traits and Immunomodulatory Properties of Leuconostoc carnosum Isolated From Meat Products

2021 ◽  
Vol 12 ◽  
Author(s):  
Stefano Raimondi ◽  
Gloria Spampinato ◽  
Francesco Candeliere ◽  
Alberto Amaretti ◽  
Paola Brun ◽  
...  
Keyword(s):  
Meat Products ◽  
Gastrointestinal Transit ◽  
Antibiotic Resistance Genes ◽  
Protective Role ◽  
Phenotypic Traits ◽  
Natural Habitats ◽  
Genes Encoding ◽  
Immunomodulatory Properties ◽  
Leuconostoc Carnosum

Twelve strains of Leuconostoc carnosum from meat products were investigated in terms of biochemical, physiological, and functional properties. The spectrum of sugars fermented by L. carnosum strains was limited to few mono- and disaccharides, consistently with the natural habitats of the species, including meat and fermented vegetables. The strains were able to grow from 4 to 37°C with an optimum of approximately 32.5°C. The ability to grow at temperatures compatible with refrigeration and in presence of up to 60 g/L NaCl explains the high loads of L. carnosum frequently described in many meat-based products. Six strains produced exopolysaccharides, causing a ropy phenotype of colonies, according to the potential involvement on L. carnosum in the appearance of slime in packed meat products. On the other side, the study provides evidence of a potential protective role of L. carnosum WC0321 and L. carnosum WC0323 against Listeria monocytogenes, consistently with the presence in these strains of the genes encoding leucocin B. Some meat-based products intended to be consumed without cooking may harbor up to 108 CFU/g of L. carnosum; therefore, we investigated the potential impact of this load on health. No strains survived the treatment with simulated gastric juice. Three selected strains were challenged for the capability to colonize a mouse model and their immunomodulatory properties were investigated. The strains did not colonize the intestine of mice during 10 days of daily dietary administration. Intriguingly, despite the loss of viability during the gastrointestinal transit, the strains exhibited different immunomodulatory effect on the maturation of dendritic cells in vivo, the extent of which correlated to the production of exopolysaccharides. The ability to stimulate the mucosal associated immune system in such probiotic-like manner, the general absence of antibiotic resistance genes, and the lack of the biosynthetic pathways for biogenic amines should reassure on the safety of this species, with potential for exploitation of selected starters.

scholarly journals Genomic Analysis of Curtobacterium Flaccumfaciens Reveals the Differences Between Pathogenic and Nonpathogenic Strains

2021 ◽  
Author(s):  
Qingde Li ◽  
Lianjun Sun
Keyword(s):  
Core Genome ◽  
Genomic Analysis ◽  
Pectate Lyase ◽  
Economic Losses ◽  
Positive Bacterium ◽  
Citrate Cycle ◽  
The Core ◽  
Genomic Level ◽  
Genes Encoding ◽  
Genome Phylogeny

Abstract Purpose Curtobacterium flaccumfaciens is a Gram-positive bacterium which has been isolated from different plants and abiotic environment. Curtobacterium. flaccumfaciens pv. flaccumfaciens (Cff) is a pathogenic bacterium that infects legume, which is causing great economic losses. At the genomic level, the metabolic and phylogenetic characteristics, and differences in pathogenicity between pathogenic and nonpathogenic C. flaccumfaciens strains have not been analyzed in detail. Methods Therefore, in order to discuss the differences in genome, phylogeny, gene function and mobile genetic elements between pathogenic and nonpathogenic strains, pangenomics and comparative genomics were used in this study to analyze 12 C. flaccumfaciens strains. Result The pangenome of C. flaccumfaciens is open. Phylogenetic analysis showed that there was no correlation between the phylogeny and pathogenicity of C. flaccumfaciens. KAAS annotation of the core genome shows that the citrate cycle was incomplete. In addition, gene islands analysis of the three pathogenicity-related genes encoding for pectate lyase, serine protease and cellulases showed that they only existed in the Cffs and LMG3645 strains. LMG3645 might be a pathogenic strain. Conclusion This study clearly and reliably revealed the differences between the pathogenic and nonpathogenic strains of C. flaccumfaciens at the genomic level, and paves the way for further research on its pathogenicity.

scholarly journals Identification and Characterization of the Genes Encoding the Core Histones and Histone Variants of Neurospora crassa

Genetics ◽  
2002 ◽  
Vol 160 (3) ◽  
pp. 961-973 ◽  
Author(s):  
Shan M Hays ◽  
Johanna Swanson ◽  
Eric U Selker
Keyword(s):  
Neurospora Crassa ◽  
Histone Variants ◽  
Null Alleles ◽  
Histone Genes ◽  
Histone H4 ◽  
Coding Regions ◽  
The Core ◽  
Genomic Arrangement ◽  
Genes Encoding ◽  
Core Histones

Abstract We have identified and characterized the complete complement of genes encoding the core histones of Neurospora crassa. In addition to the previously identified pair of genes that encode histones H3 and H4 (hH3 and hH4-1), we identified a second histone H4 gene (hH4-2), a divergently transcribed pair of genes that encode H2A and H2B (hH2A and hH2B), a homolog of the F/Z family of H2A variants (hH2Az), a homolog of the H3 variant CSE4 from Saccharomyces cerevisiae (hH3v), and a highly diverged H4 variant (hH4v) not described in other species. The hH4-1 and hH4-2 genes, which are 96% identical in their coding regions and encode identical proteins, were inactivated independently. Strains with inactivating mutations in either gene were phenotypically wild type, in terms of growth rates and fertility, but the double mutants were inviable. As expected, we were unable to isolate null alleles of hH2A, hH2B, or hH3. The genomic arrangement of the histone and histone variant genes was determined. hH2Az and the hH3-hH4-1 gene pair are on LG IIR, with hH2Az centromere-proximal to hH3-hH4-1 and hH3 centromere-proximal to hH4-1. hH3v and hH4-2 are on LG IIIR with hH3v centromere-proximal to hH4-2. hH4v is on LG IVR and the hH2A-hH2B pair is located immediately right of the LG VII centromere, with hH2A centromere-proximal to hH2B. Except for the centromere-distal gene in the pairs, all of the histone genes are transcribed toward the centromere. Phylogenetic analysis of the N. crassa histone genes places them in the Euascomycota lineage. In contrast to the general case in eukaryotes, histone genes in euascomycetes are few in number and contain introns. This may be a reflection of the evolution of the RIP (repeat-induced point mutation) and MIP (methylation induced premeiotically) processes that detect sizable duplications and silence associated genes.

scholarly journals Influence of spatial structure on protein damage susceptibility: a bioinformatics approach

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maximilian Fichtner ◽  
Stefan Schuster ◽  
Heiko Stark
Keyword(s):  
Amino Acids ◽  
Molecular Medicine ◽  
Protein Damage ◽  
Aging Research ◽  
Form And Function ◽  
The Core ◽  
And Function ◽  
Thermophilic Organisms ◽  
Damage Susceptibility ◽  
Protein Shell

AbstractAging research is a very popular field of research in which the deterioration or decline of various physiological features is studied. Here we consider the molecular level, which can also have effects on the macroscopic level. The proteinogenic amino acids differ in their susceptibilities to non-enzymatic modification. Some of these modifications can lead to protein damage and thus can affect the form and function of proteins. For this, it is important to know the distribution of amino acids between the protein shell/surface and the core. This was investigated in this study for all known structures of peptides and proteins available in the PDB. As a result, it is shown that the shell contains less susceptible amino acids than the core with the exception of thermophilic organisms. Furthermore, proteins could be classified according to their susceptibility. This can then be used in applications such as phylogeny, aging research, molecular medicine, and synthetic biology.

scholarly journals Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils

2021 ◽  
Author(s):  
Adrian Gorecki ◽  
Stine Holm ◽  
Mikolaj Dziurzynski ◽  
Matthias Winkel ◽  
Sizhong Yang ◽  
...  
Keyword(s):  
Active Layer ◽  
Bacterial Communities ◽  
Extraction Methods ◽  
Metal Resistance ◽  
Rapid Adaptation ◽  
Tundra Soils ◽  
Genetic Traits ◽  
Functional Potential ◽  
Stress Response Genes ◽  
Genes Encoding

AbstractPlasmids have the potential to transfer genetic traits within bacterial communities and thereby serve as a crucial tool for the rapid adaptation of bacteria in response to changing environmental conditions. Our knowledge of the environmental pool of plasmids (the metaplasmidome) and encoded functions is still limited due to a lack of sufficient extraction methods and tools for identifying and assembling plasmids from metagenomic datasets. Here, we present the first insights into the functional potential of the metaplasmidome of permafrost-affected active-layer soil—an environment with a relatively low biomass and seasonal freeze–thaw cycles that is strongly affected by global warming. The obtained results were compared with plasmid-derived sequences extracted from polar metagenomes. Metaplasmidomes from the Siberian active layer were enriched via cultivation, which resulted in a longer contig length as compared with plasmids that had been directly retrieved from the metagenomes of polar environments. The predicted hosts of plasmids belonged to Moraxellaceae, Pseudomonadaceae, Enterobacteriaceae, Pectobacteriaceae, Burkholderiaceae, and Firmicutes. Analysis of their genetic content revealed the presence of stress-response genes, including antibiotic and metal resistance determinants, as well as genes encoding protectants against the cold.

scholarly journals A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

2008 ◽  
Vol 191 (1) ◽  
pp. 91-99 ◽  
Author(s):  
Marc Deloger ◽  
Meriem El Karoui ◽  
Marie-Agnès Petit
Keyword(s):  
Dna Sequences ◽  
Dna Content ◽  
Core Genome ◽  
Biological Diversity ◽  
Bacterial Species ◽  
Genomic Distance ◽  
The Core ◽  
Intraspecies Diversity ◽  
Genome Level ◽  
Definition Of

ABSTRACT The fundamental unit of biological diversity is the species. However, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. Two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ANI), which detects the DNA conservation of the core genome, and the DNA content, which calculates the proportion of DNA shared by two genomes. Both estimates are based on BLAST alignments for the definition of DNA sequences common to the genome pair. Interestingly, however, results using these methods on intraspecies pairs are not well correlated. This prompted us to develop a genomic-distance index taking into account both criteria of diversity, which are based on DNA maximal unique matches (MUM) shared by two genomes. The values, called MUMi, for MUM index, correlate better with the ANI than with the DNA content. Moreover, the MUMi groups strains in a way that is congruent with routinely used multilocus sequence-typing trees, as well as with ANI-based trees. We used the MUMi to determine the relatedness of all available genome pairs at the species and genus levels. Our analysis reveals a certain consistency in the current notion of bacterial species, in that the bulk of intraspecies and intragenus values are clearly separable. It also confirms that some species are much more diverse than most. As the MUMi is fast to calculate, it offers the possibility of measuring genome distances on the whole database of available genomes.

scholarly journals Deciphering the Enigma of the Histone H2A.Z-1/H2A.Z-2 Isoforms: Novel Insights and Remaining Questions

Cells ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 1167
Author(s):  
Manjinder S. Cheema ◽  
Katrina V. Good ◽  
Bohyun Kim ◽  
Heddy Soufari ◽  
Connor O’Sullivan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Dna Damage ◽  
Chromosome Segregation ◽  
Multiple Roles ◽  
Histone H2a ◽  
The Core ◽  
Structural Differences ◽  
Functional Involvement ◽  
Insight Into

The replication independent (RI) histone H2A.Z is one of the more extensively studied variant members of the core histone H2A family, which consists of many replication dependent (RD) members. The protein has been shown to be indispensable for survival, and involved in multiple roles from DNA damage to chromosome segregation, replication, and transcription. However, its functional involvement in gene expression is controversial. Moreover, the variant in several groups of metazoan organisms consists of two main isoforms (H2A.Z-1 and H2A.Z-2) that differ in a few (3–6) amino acids. They comprise the main topic of this review, starting from the events that led to their identification, what is currently known about them, followed by further experimental, structural, and functional insight into their roles. Despite their structural differences, a direct correlation to their functional variability remains enigmatic. As all of this is being elucidated, it appears that a strong functional involvement of isoform variability may be connected to development.

scholarly journals To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites

2021 ◽  
Vol 377 (1842) ◽  
Author(s):  
Jorge A. Moura de Sousa ◽  
Eduardo P. C. Rocha
Keyword(s):  
Escherichia Coli ◽  
Molecular Mechanisms ◽  
Core Genome ◽  
Mobile Genetic Elements ◽  
Abundance Distribution ◽  
Theme Issue ◽  
Genetic Elements ◽  
The Core ◽  
Antagonistic Interactions ◽  
Variable Genes

Bacteriophages (phages) are bacterial parasites that can themselves be parasitized by phage satellites. The molecular mechanisms used by satellites to hijack phages are sometimes understood in great detail, but the origins, abundance, distribution and composition of these elements are poorly known. Here, we show that P4-like elements are present in more than 30% of the genomes of Enterobacterales, and in almost half of those of Escherichia coli , sometimes in multiple distinct copies. We identified over 1000 P4-like elements with very conserved genetic organization of the core genome and a few hotspots with highly variable genes. These elements are never found in plasmids and have very little homology to known phages, suggesting an independent evolutionary origin. Instead, they are scattered across chromosomes, possibly because their integrases are often exchanged with other elements. The rooted phylogenies of hijacking functions are correlated and suggest longstanding coevolution. They also reveal broad host ranges in P4-like elements, as almost identical elements can be found in distinct bacterial genera. Our results show that P4-like phage satellites constitute a very distinct, widespread and ancient family of mobile genetic elements. They pave the way for studying the molecular evolution of antagonistic interactions between phages and their satellites. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

Biosynthesis of Carbohydrates and Amino Acids

2016 ◽  
Author(s):  
Gary W. Morrow
Keyword(s):  
Amino Acids ◽  
Construction Materials ◽  
Building Blocks ◽  
General Term ◽  
Molecular Formula ◽  
Biosynthetic Pathways ◽  
Hydrated Form ◽  
The Core ◽  
Carbon Dioxide Co2 ◽  
Structure And Metabolism

We have already seen that some of the basic building blocks used in the biosynthesis of natural products are amino acids such as phenylalanine, tyrosine, and others. These and other crucial construction materials such as the acyl group in acetyl-CoA are all ultimately derived from carbohydrates. In this chapter, we will present an abbreviated overview of the components of carbohydrate structure and metabolism sufficient for our purposes going forward, with a schematic flowchart showing how carbohydrates and amino acids are modified, combined, and branched off in various ways to yield the distinct set of biosynthetic pathways that will form the core of the remainder of the text. We will finish the chapter with a brief, general review of amino acid nomenclature and structure with emphasis on the key amino acids that will be used throughout the remainder of the text. We know that plants make glucose (C6H12O6) by photosynthesis using light, water (H2O), and carbon dioxide (CO2). Another way of looking at the formula for glucose is C6(H2O)6, that is, six carbon atoms and six water molecules. Thus, glucose was originally referred to as a hydrated form of carbon—a carbohydrate. But this is a very general term since there are many different types of carbohydrate compounds. One way to broadly classify carbohydrates is to identify them as either mono- (one), di- (two), oligo- (a few) or poly- (many) saccharides. For example, glucose (C6H12O6) cannot be broken down into simpler carbohydrates by simple hydrolysis, so it is classified as a monosaccharide, that is, a single, discrete carbohydrate compound. On the other hand, the carbohydrate sucrose (C12H22O11) is classified as a disaccharide since when it is subjected to aqueous hydrolysis, it yields two different monosaccharide carbohydrates, namely glucose (C6H12O6) and fructose (C6H12O6). Noting that glucose and fructose are different compounds but with the same molecular formula, they must be related to one another either as stereoisomers or as constitutional isomers, so further refinement of classification is needed. Structurally speaking, most monosaccharide carbohydrates are simply polyhydroxyaldehydes (aldoses) or polyhydroxyketones (ketoses) which can be further classified using a combination of aldo- or keto- prefixes along with suffixes such as triose, tetrose, pentose, or hexose to designate the number of carbon atoms.

Consistency and Change

2019 ◽  
Author(s):  
Alan Kelly
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Living Organism ◽  
Peptide Bond ◽  
The Body ◽  
Blood Proteins ◽  
Genes Encoding ◽  
Fundamental Phenomenon ◽  
P Proteins

Proteins are, in my view, the most impressive molecules in food. They influence the texture, crunch, chew, flow, color, flavor, and nutritional quality of food. Not only that, but they can radically change their properties and how they behave depending on the environment and, critically for food, in response to processes like heating. Even when broken down into smaller components they are important, for example giving cheese many of its critical flavor notes. Indeed, I would argue that perhaps the most fundamental phenomenon we encounter in cooking or processing food is the denaturation of proteins, as will be explained shortly. Beyond food, the value of proteins and their properties is widespread across biology. Many of the most significant molecules in our body and that of any living organism (including plants and animals) are proteins. These include those that make hair and skin what they are, as well as the hemoglobin that transports oxygen around the body in our blood. Proteins are built from amino acids, a family of 20 closely related small molecules, which all have in chemical terms the same two ends (chemically speaking, an amino end and an acidic end, hence the name) but differ in the middle. This bit in the middle varies from amino acid to amino acid, from simple (a hydrogen atom in the case of glycine, the simplest amino acid) to much more complex structures. Amino acids can link up very neatly, as the amino end of one can form a bond (called a peptide bond) with the acid end of another, and so forth, so that chains of amino acids are formed that, when big enough (more than a few dozen amino acids), we call proteins. Our bodies produce thousands of proteins for different functions, and the instructions for which amino acids combine to make which proteins are essentially what the genetic code encrypted in our DNA specifies. We hear a lot about our genes encoding the secrets of life, but what that code spells is basically P-R-O-T-E-I-N. Yes, these are very important molecules!

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