Phylogenetic signal and functional categories in Proteobacteria genomes

BACKGROUND: A comprehensive evolutionary analysis of bacterial genomes implies to identify the hallmark of vertical and non-vertical signals and to discriminate them from the presence of mere phylogenetic noise. In this report we have addressed the impact of factors like the universal distribution of the genes, their essentiality or their functional role in the cell on the inference of vertical signal through phylogenomic methods. RESULTS: We have established that supermatrices derived from data sets composed mainly by genes suspected to be essential for bacterial cellular life perform better on the recovery of vertical signal than those composed by widely distributed genes. In addition, we show that the "Transcription" category of genes seems to harbor a better vertical signal than other functional categories. Moreover, the "Poorly characterized" category performs better than other categories related with metabolism or cellular processes. CONCLUSION: From these results we conclude that different data sets allow addressing different questions in phylogenomic analyses. The vertical signal seems to be more present in essential genes although these also include a significant degree of incongruence. From a functional perspective, as expected, informational genes perform better than operational ones but we have also shown the surprising behavior of poorly annotated genes, which points to their importance in the genome evolution of bacteria

Unraveling the evolutionary history of the phosphoryl-transfer chain of the phosphoenolpyruvate:phosphotransferase system through phylogenetic analyses and genome context

<p>Abstract</p> <p>Background</p> <p>The phosphoenolpyruvate phosphotransferase system (PTS) plays a major role in sugar transport and in the regulation of essential physiological processes in many bacteria. The PTS couples solute transport to its phosphorylation at the expense of phosphoenolpyruvate (PEP) and it consists of general cytoplasmic phosphoryl transfer proteins and specific enzyme II complexes which catalyze the uptake and phosphorylation of solutes. Previous studies have suggested that the evolution of the constituents of the enzyme II complexes has been driven largely by horizontal gene transfer whereas vertical inheritance has been prevalent in the general phosphoryl transfer proteins in some bacterial groups. The aim of this work is to test this hypothesis by studying the evolution of the phosphoryl transfer proteins of the PTS.</p> <p>Results</p> <p>We have analyzed the evolutionary history of the PTS phosphoryl transfer chain (PTS-ptc) components in 222 complete genomes by combining phylogenetic methods and analysis of genomic context. Phylogenetic analyses alone were not conclusive for the deepest nodes but when complemented with analyses of genomic context and functional information, the main evolutionary trends of this system could be depicted.</p> <p>Conclusion</p> <p>The PTS-ptc evolved in bacteria after the divergence of early lineages such as <it>Aquificales</it>, <it>Thermotogales </it>and <it>Thermus/Deinococcus</it>. The subsequent evolutionary history of the PTS-ptc varied in different bacterial lineages: vertical inheritance and lineage-specific gene losses mainly explain the current situation in <it>Actinobacteria </it>and <it>Firmicutes </it>whereas horizontal gene transfer (HGT) also played a major role in <it>Proteobacteria</it>. Most remarkably, we have identified a HGT event from <it>Firmicutes </it>or <it>Fusobacteria </it>to the last common ancestor of the <it>Enterobacteriaceae</it>, <it>Pasteurellaceae</it>, <it>Shewanellaceae </it>and <it>Vibrionaceae</it>. This transfer led to extensive changes in the metabolic and regulatory networks of these bacteria including the development of a novel carbon catabolite repression system. Hence, this example illustrates that HGT can drive major physiological modifications in bacteria.</p

Draft genome sequence of Mycobacterium brumae ATCC 51384

Here, we report the draft genome sequence of Mycobacterium brumae type strain ATCC 51384. This is the first draft genome sequence of M. brumae, a nonpathogenic, rapidly growing, nonchromogenic mycobacterium, with immunotherapeutic capacities

Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis.

Deciphering physiological changes that mediate transition of Mycobacterium tuberculosis between replicating and nonreplicating states is essential to understanding how the pathogen can persist in an individual host for decades. We have combined RNA sequencing (RNA-seq) of 5' triphosphate-enriched libraries with regular RNA-seq to characterize the architecture and expression of M. tuberculosis promoters. We identified over 4,000 transcriptional start sites (TSSs). Strikingly, for 26% of the genes with a primary TSS, the site of transcriptional initiation overlapped with the annotated start codon, generating leaderless transcripts lacking a 5' UTR and, hence, the Shine-Dalgarno sequence commonly used to initiate ribosomal engagement in eubacteria. Genes encoding proteins with active growth functions were markedly depleted from the leaderless transcriptome, and there was a significant increase in the overall representation of leaderless mRNAs in a starvation model of growth arrest. The high percentage of leaderless genes may have particular importance in the physiology of nonreplicating M. tuberculosis

Evaluation of two different concentration methods for surveillance of human viruses in sewage and their effects on SARS-CoV-2 sequencing

During the current COVID-19 pandemic, wastewater-based epidemiology (WBE) emerged as a reliable strategy both as a surveillance method and a way to provide an overview of the SARS-CoV-2 variants circulating among the population. Our objective was to compare two different concentration methods, a well-established aluminum-based procedure (AP) and the commercially available Maxwell® RSC Enviro Wastewater TNA Kit (TNA) for human enteric virus, viral indicators and SARS-CoV-2 surveillance. Additionally, both concentration methods were analyzed for their impact on viral infectivity, and nucleic acids obtained from each method were also evaluated by massive sequencing for SARS-CoV-2. The percentage of SARS-CoV-2 positive samples using the AP method accounted to 100 %, 83.3 %, and 33.3 % depending on the target region while 100 % positivity for these same three target regions was reported using the TNA procedure. The concentrations of norovirus GI, norovirus GII and HEV using the TNA method were significantly greater than for the AP method while no differences were reported for rotavirus, astrovirus, crAssphage and PMMoV. Furthermore, TNA kit in combination with the Artic v4 primer scheme yields the best SARS-CoV-2 sequencing results. Regarding impact on infectivity, the concentration method used by the TNA kit showed near-complete lysis of viruses. Our results suggest that although the performance of the TNA kit was higher than that of the aluminum procedure, both methods are suitable for the analysis of enveloped and non-enveloped viruses in wastewater by molecular methods

Draft genome sequences of Mycobacterium setense type strain DSM-45070 and the nonpathogenic strain Manresensis, isolated from the bank of the Cardener river in Manresa, Catalonia, Spain

This study was funded by the Spanish Government, Instituto de Salud Carlos III (ISCIII), through the CIBER CRP-TB and the FIS 011/01702 grants to PJC, and by Manresana de Micobacteriologia, s.l. Additional support came from IMPPC core funding from the Generalitat de Catalunya to LS. JV, GR, SS, were funded by grant ADE10/00026 from ISCIII. JV was also co-funded by ISIS contract II11/00014 from ISCIII. IC is supported by the Spanish Ministerio de Economia y Competitividad (MINECO) through a Ramón y Cajal contract RYC-2012-10627 and grant SAF2013-43521-R. E.J. was funded by Instituto de Salud Carlos III-PI1001438 and the European Regional Development Fund (FEDER), and CV by Miguel Servet Contract CP13/00174.We present here the draft genome sequences of two Mycobacterium setense strains. One of them corresponds to the M. setense type strain DSM-45070, originally isolated from a patient with a posttraumatic chronic skin abscess. The other one corresponds to the nonpathogenic M. setense strain Manresensis, isolated from the Cardener River crossing Manresa, Catalonia, Spain. A comparative genomic analysis shows a smaller genome size and fewer genes in M. setense strain Manresensis relative to those of the type strain, and it shows the genome segments unique to each strain

Genome-wide mutational biases fuel transcriptional diversity in the Mycobacterium tuberculosis complex

Abstract: The Mycobacterium tuberculosis complex (MTBC) members display different host-specificities and virulence phenotypes. Here, we have performed a comprehensive RNAseq and methylome analysis of the main clades of the MTBC and discovered unique transcriptional profiles. The majority of genes differentially expressed between the clades encode proteins involved in host interaction and metabolic functions. A significant fraction of changes in gene expression can be explained by positive selection on single mutations that either create or disrupt transcriptional start sites (TSS). Furthermore, we show that clinical strains have different methyltransferases inactivated and thus different methylation patterns. Under the tested conditions, differential methylation has a minor direct role on transcriptomic differences between strains. However, disruption of a methyltransferase in one clinical strain revealed important expression differences suggesting indirect mechanisms of expression regulation. Our study demonstrates that variation in transcriptional profiles are mainly due to TSS mutations and have likely evolved due to differences in host characteristics

TweetNorm: a benchmark for lexical normalization of spanish tweets

The language used in social media is often characterized by the abundance of informal and non-standard writing. The normalization of this non-standard language can be crucial to facilitate the subsequent textual processing and to consequently help boost the performance of natural language processing tools applied to social media text. In this paper we present a benchmark for lexical normalization of social media posts, specifically for tweets in Spanish language. We describe the tweet normalization challenge we organized recently, analyze the performance achieved by the different systems submitted to the challenge, and delve into the characteristics of systems to identify the features that were useful. The organization of this challenge has led to the production of a benchmark for lexical normalization of social media, including an evaluation framework, as well as an annotated corpus of Spanish tweets-TweetNorm_es-, which we make publicly available. The creation of this benchmark and the evaluation has brought to light the types of words that submitted systems did best with, and posits the main shortcomings to be addressed in future work.Postprint (published version

Draft genome sequences of Mycobacterium setense type strain DSM-45070 and the nonpathogenic strain Manresensis, isolated from the bank of the Cardener River in Manresa, Catalonia, Spain

We present here the draft genome sequences of two Mycobacterium setense strains. One of them corresponds to the M. setense type strain DSM-45070, originally isolated from a patient with a posttraumatic chronic skin abscess. The other one corresponds to the nonpathogenic M. setense strain Manresensis, isolated from the Cardener River crossing Manresa, Catalonia, Spain. A comparative genomic analysis shows a smaller genome size and fewer genes in M. setense strain Manresensis relative to those of the type strain, and it shows the genome segments unique to each strain