scholarly journals Novel start codons introduce novel coding sequences in the human genomes

2020 ◽  
Author(s):  
He Zhang ◽  
Yang Xie
Keyword(s):  
Translation Initiation ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Human Populations ◽  
The Novel ◽  
Coding Sequences ◽  
Human Genomes ◽  
High Level ◽  
Selection Signal ◽  
Human Specific

AbstractStart-gain mutations can introduce novel start codons and generate novel coding sequences that may affect the function of genes. In this study, we systematically investigated the novel start codons that were either polymorphic or fixed in the human genomes. 829 polymorphic start-gain SNVs were identified in the human populations, and the novel start codons introduced by these SNVs have significantly higher activity in translation initiation. Some of these start-gain SNVs were reported to be associated with phenotypes and diseases in previous studies. By comparative genomic analysis, we found 26 human-specific start codons that were fixed after the divergence between the human and chimpanzee, and high-level translation initiation activity was observed on them. The negative selection signal was detected in the novel coding sequences introduced by these human-specific start codons, indicating the important function of these novel coding sequences. This study reveals start-gain mutations are keeping appearing in the human genomes during the evolution and may be important sources altering the function of genes which may further affect the phenotypes or cause diseases.

scholarly journals High-Level Aminoglycoside Resistance in Human Clinical Klebsiella pneumoniae Complex Isolates and Characteristics of armA-Carrying IncHI5 Plasmids

2021 ◽  
Vol 12 ◽  
Author(s):  
Xueya Zhang ◽  
Qiaoling Li ◽  
Hailong Lin ◽  
Wangxiao Zhou ◽  
Changrui Qian ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Resistance Genes ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Conjugative Plasmid ◽  
Comparative Genomic ◽  
Aminoglycoside Resistance ◽  
Life Threatening ◽  
Aminoglycoside Resistance Genes ◽  
High Level

Aminoglycosides are important options for treating life-threatening infections. However, high levels of aminoglycoside resistance (HLAR) among Klebsiella pneumoniae isolates have been observed to be increasing frequently. In this study, a total of 292 isolates of the K. pneumoniae complex from a teaching hospital in China were analyzed. Among these isolates, the percentage of HLAR strains was 13.7% (40/292), and 15 aminoglycoside resistance genes were identified among the HLAR strains, with rmtB being the most dominant resistance gene (70%, 28/40). We also described an armA-carrying Klebsiella variicola strain KP2757 that exhibited a high-level resistance to all aminoglycosides tested. Whole-genome sequencing of KP2757 demonstrated that the strain contained one chromosome and three plasmids, with all the aminoglycoside resistance genes (including two copies of armA and six AME genes) being located on a conjugative plasmid, p2757-346, belonging to type IncHI5. Comparative genomic analysis of eight IncHI5 plasmids showed that six of them carried two copies of the intact armA gene in the complete or truncated Tn1548 transposon. To the best of our knowledge, for the first time, we observed that two copies of armA together with six AME genes coexisted on the same plasmid in a strain of K. variicola with HLAR. Comparative genomic analysis of eight armA-carrying IncHI5 plasmids isolated from humans and sediment was performed, suggesting the potential for dissemination of these plasmids among bacteria from different sources. These results demonstrated the necessity of monitoring the prevalence of IncHI5 plasmids to restrict their worldwide dissemination.

scholarly journals Comparative genomic analysis of eutherian connexin genes

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Marko Premzl
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Data Sets ◽  
Data Set ◽  
Coding Sequences ◽  
Gene Annotations ◽  
Connexin Gene ◽  
Connexin Genes ◽  
Gene Data

AbstractThe eutherian connexins were characterized as protein constituents of gap junctions implicated in cell-cell communications between adjoining cells in multiple cell types, regulation of major physiological processes and disease pathogeneses. However, conventional connexin gene and protein classifications could be regarded as unsuitable in descriptions of comprehensive eutherian connexin gene data sets, due to ambiguities and inconsistencies in connexin gene and protein nomenclatures. Using eutherian comparative genomic analysis protocol and 35 public eutherian reference genomic sequence data sets, the present analysis attempted to update and revise comprehensive eutherian connexin gene data sets, and address and resolve major discrepancies in their descriptions. Among 631 potential coding sequences, the tests of reliability of eutherian public genomic sequences annotated, in aggregate, 349 connexin complete coding sequences. The most comprehensive curated eutherian connexin gene data set described 21 major gene clusters, 4 of which included evidence of differential gene expansions. For example, the present gene annotations initially described human CXNK1 gene and annotated 22 human connexin genes. Phylogenetic tree calculations and calculations of pairwise nucleotide sequence identity patterns proposed revised and updated phylogenetic classification of eutherian connexin genes. Therefore, the present study integrating gene annotations, phylogenetic analysis and protein molecular evolution analysis proposed new nomenclature of eutherian connexin genes and proteins.

scholarly journals Role of Hypermutability in the Evolution of the Genus Oenococcus

2007 ◽  
Vol 190 (2) ◽  
pp. 564-570 ◽  
Author(s):  
Angela M. Marcobal ◽  
David A. Sela ◽  
Yuri I. Wolf ◽  
Kira S. Makarova ◽  
David A. Mills
Keyword(s):  
Lactic Acid ◽  
Leuconostoc Mesenteroides ◽  
Genomic Analysis ◽  
Oenococcus Oeni ◽  
Mutation Rates ◽  
Comparative Genomic ◽  
Allelic Polymorphism ◽  
Resistant Strains ◽  
High Level

ABSTRACT Oenococcus oeni is an alcohol-tolerant, acidophilic lactic acid bacterium primarily responsible for malolactic fermentation in wine. A recent comparative genomic analysis of O. oeni PSU-1 with other sequenced lactic acid bacteria indicates that PSU-1 lacks the mismatch repair (MMR) genes mutS and mutL. Consistent with the lack of MMR, mutation rates for O. oeni PSU-1 and a second oenococcal species, O. kitaharae, were higher than those observed for neighboring taxa, Pediococcus pentosaceus and Leuconostoc mesenteroides. Sequence analysis of the rpoB mutations in rifampin-resistant strains from both oenococcal species revealed a high percentage of transition mutations, a result indicative of the lack of MMR. An analysis of common alleles in the two sequenced O. oeni strains, PSU-1 and BAA-1163, also revealed a significantly higher level of transition substitutions than were observed in other Lactobacillales species. These results suggest that the genus Oenococcus is hypermutable due to the loss of mutS and mutL, which occurred with the divergence away from the neighboring Leuconostoc branch. The hypermutable status of the genus Oenococcus explains the observed high level of allelic polymorphism among known O. oeni isolates and likely contributed to the unique adaptation of this genus to acidic and alcoholic environments.

scholarly journals Evidence that Human Chlamydia pneumoniae Was Zoonotically Acquired

2009 ◽  
Vol 191 (23) ◽  
pp. 7225-7233 ◽  
Author(s):  
G. S. A. Myers ◽  
S. A. Mathews ◽  
M. Eppinger ◽  
C. Mitchell ◽  
K. K. O'Brien ◽  
...  
Keyword(s):  
Chlamydia Pneumoniae ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Human Populations ◽  
Animal Reservoir ◽  
Single Nucleotide ◽  
Phascolarctos Cinereus ◽  
Zoonotic Infections ◽  
Conserved Genes ◽  
Animal Isolate

ABSTRACT Zoonotic infections are a growing threat to global health. Chlamydia pneumoniae is a major human pathogen that is widespread in human populations, causing acute respiratory disease, and has been associated with chronic disease. C. pneumoniae was first identified solely in human populations; however, its host range now includes other mammals, marsupials, amphibians, and reptiles. Australian koalas (Phascolarctos cinereus) are widely infected with two species of Chlamydia, C. pecorum and C. pneumoniae. Transmission of C. pneumoniae between animals and humans has not been reported; however, two other chlamydial species, C. psittaci and C. abortus, are known zoonotic pathogens. We have sequenced the 1,241,024-bp chromosome and a 7.5-kb cryptic chlamydial plasmid of the koala strain of C. pneumoniae (LPCoLN) using the whole-genome shotgun method. Comparative genomic analysis, including pseudogene and single-nucleotide polymorphism (SNP) distribution, and phylogenetic analysis of conserved genes and SNPs against the human isolates of C. pneumoniae show that the LPCoLN isolate is basal to human isolates. Thus, we propose based on compelling genomic and phylogenetic evidence that humans were originally infected zoonotically by an animal isolate(s) of C. pneumoniae which adapted to humans primarily through the processes of gene decay and plasmid loss, to the point where the animal reservoir is no longer required for transmission.

scholarly journals Isolation, characterization, and comparative genomic analysis of a phage infecting high-level aminoglycoside-resistant (HLAR) Enterococcus faecalis

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9171 ◽  
Author(s):  
Danial Nasr Azadani ◽  
Daiyuan Zhang ◽  
J. Robert Hatherill ◽  
David Silva ◽  
Jeffrey W. Turner
Keyword(s):  
Genome Sequencing ◽  
Large Subunit ◽  
Gc Content ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Single Locus ◽  
Comparative Genomic ◽  
Antibiotic Resistant ◽  
High Level ◽  
High Degree

Enterococcus is a genus of Gram-positive bacteria that are commensal to the gastrointestinal tracts of humans but some species have been increasingly implicated as agents of nosocomial infections. The increase in infections and the spread of antibiotic-resistant strains have contributed to renewed interest in the discovery of Enterococcus phages. The aims of this study were (1) the isolation, characterization, and genome sequencing of a phage capable of infecting an antibiotic-resistant E. faecalis strain, and (2) the comparative genomic analysis of publicly-available Enterococcus phages. For this purpose, multiple phages were isolated from wastewater treatment plant (WWTP) influent using a high-level aminoglycoside-resistant (HLAR) E. faecalis strain as the host. One phage, phiNASRA1, demonstrated a high lytic efficiency (∼97.52%). Transmission electron microscopy (TEM) and whole-genome sequencing (WGS) showed that phiNASRA1 belongs to the Siphoviridae family of double-stranded DNA viruses. The phage was approximately 250 nm in length and its complete genome (40,139 bp, 34.7% GC) contained 62 open reading frames (ORFs). Phylogenetic comparisons of phiNASRA1 and 31 publicly-available Enterococcus phages, based on the large subunit terminase and portal proteins, grouped phage by provenance, size, and GC content. In particular, both phylogenies grouped phages larger than 100 kbp into distinct clades. A phylogeny based on a pangenome analysis of the same 32 phages also grouped phages by provenance, size, and GC content although agreement between the two single-locus phylogenies was higher. Per the pangenome phylogeny, phiNASRA1 was most closely related to phage LY0322 that was similar in size, GC content, and number of ORFs (40,139 and 40,934 bp, 34.77 and 34.80%, and 60 and 64 ORFs, respectively). The pangenome analysis did illustrate the high degree of sequence diversity and genome plasticity as no coding sequence was homologous across all 32 phages, and even ‘conserved’ structural proteins (e.g., the large subunit terminase and portal proteins) were homologous in no more than half of the 32 phage genomes. These findings contribute to a growing body of literature devoted to understanding phage biology and diversity. We propose that this high degree of diversity limited the value of the single-locus and pangenome phylogenies. By contrast, the high degree of homology between phages larger than 100 kbp suggests that pangenome analyses of more similar phages is a viable method for assessing subclade diversity. Future work is focused on validating phiNASRA1 as a potential therapeutic agent to eradicate antibiotic-resistant E. faecalis infections in an animal model.

scholarly journals Rediscovering a Forgotten System of Symbiosis: Historical Perspective and Future Potential

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1063
Author(s):  
Vincent G. Martinson
Keyword(s):  
Historical Perspective ◽  
Sequence Divergence ◽  
Genomic Analysis ◽  
Model Systems ◽  
Recent Common Ancestor ◽  
Comparative Genomic ◽  
Human Populations ◽  
Candida Auris ◽  
Most Recent Common Ancestor ◽  
Recent Emergence

While the majority of symbiosis research is focused on bacteria, microbial eukaryotes play important roles in the microbiota and as pathogens, especially the incredibly diverse Fungi kingdom. The recent emergence of widespread pathogens in wildlife (bats, amphibians, snakes) and multidrug-resistant opportunists in human populations (Candida auris) has highlighted the importance of better understanding animal–fungus interactions. Regardless of their prominence there are few animal–fungus symbiosis models, but modern technological advances are allowing researchers to utilize novel organisms and systems. Here, I review a forgotten system of animal–fungus interactions: the beetle–fungus symbioses of Drugstore and Cigarette beetles with their symbiont Symbiotaphrina. As pioneering systems for the study of mutualistic symbioses, they were heavily researched between 1920 and 1970, but have received only sporadic attention in the past 40 years. Several features make them unique research organisms, including (1) the symbiont is both extracellular and intracellular during the life cycle of the host, and (2) both beetle and fungus can be cultured in isolation. Specifically, fungal symbionts intracellularly infect cells in the larval and adult beetle gut, while accessory glands in adult females harbor extracellular fungi. In this way, research on the microbiota, pathogenesis/infection, and mutualism can be performed. Furthermore, these beetles are economically important stored-product pests found worldwide. In addition to providing a historical perspective of the research undertaken and an overview of beetle biology and their symbiosis with Symbiotaphrina, I performed two analyses on publicly available genomic data. First, in a preliminary comparative genomic analysis of the fungal symbionts, I found striking differences in the pathways for the biosynthesis of two B vitamins important for the host beetle, thiamine and biotin. Second, I estimated the most recent common ancestor for Drugstore and Cigarette beetles at 8.8–13.5 Mya using sequence divergence (CO1 gene). Together, these analyses demonstrate that modern methods and data (genomics, transcriptomes, etc.) have great potential to transform these beetle–fungus systems into model systems again.

scholarly journals Bradymonabacteria, a novel bacterial predator with versatile survival strategies in saline environments

2020 ◽  
Author(s):  
Da-Shuai Mu ◽  
Shuo Wang ◽  
Qi-Yun Liang ◽  
Zhao-Zhong Du ◽  
Renmao Tian ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Amplicon Sequencing ◽  
Survival Strategies ◽  
Comparative Genomic ◽  
The Novel ◽  
Saline Environments ◽  
16S Rrna Amplicon Sequencing ◽  
High Preference ◽  
Predatory Bacteria ◽  
Potential Contact

Abstract Background: Bacterial predation is an important selective force for microbial community structure and dynamics. However, only a limited number of predatory bacteria were reported, and their predatory strategies and evolutionary adaption remain elusive. We recently isolated a novel group of bacterial predator, Bradymonabacteria, representative of the novel order Bradymonadales in δ-Proteobacteria. Compared with other bacterial predators (e.g. Myxococcales and Bdellovibrionales), the predatory and living strategies of Bradymonadales remain largely unknown.Results: Bradymonabacteria preyed on diverse bacteria but had a high preference on Bacteroidetes based on individual co-culture of Bradymonabacteria with 281 prey bacteria. Genomic analysis of 13 recently sequenced Bradymonabacteria indicated that these bacteria had conspicuous metabolic deficiencies, but they could synthesize many polymers, such as polyphosphate and polyhydroxyalkanoates. Dual-transcriptome analysis of co-culture of Bradymonabacteria and prey suggested the potential contact-dependent predation mechanism. Comparative genomic analysis with other 24 bacterial predators indicated Bradymonabacteria had different predatory and living strategies. Furthermore, we extracted Bradymonadales from 1552 public available 16S rRNA amplicon sequencing samples and found that Bradymonadales was widely distributed and highly abundant in saline environments. Phylogenetic analysis showed there may be six proposed subgroups for this order and each subgroup occupied a different habitat. Conclusions: Bradymonabacteria have unique living strategies, which are different from so-called “obligate” or “facultative” predators. We propose a framework to categorize the current bacterial predators into 3 groups: (i) highly prey-dependent predators, (ii) facultative prey-dependent predators, and (iii) prey-independent predators. Our findings provide an ecological and evolutionary framework for Bradymonadales and highlight their potential ecological roles in saline environments.

scholarly journals Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments

2020 ◽  
Author(s):  
Da-Shuai Mu ◽  
Shuo Wang ◽  
Qi-Yun Liang ◽  
Zhao-Zhong Du ◽  
Renmao Tian ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Amplicon Sequencing ◽  
Survival Strategies ◽  
Comparative Genomic ◽  
The Novel ◽  
Saline Environments ◽  
16S Rrna Amplicon Sequencing ◽  
High Preference ◽  
Predatory Bacteria ◽  
Potential Contact

Abstract Background: Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Bradymonabacteria, representative of the novel order Bradymonadales in δ-Proteobacteria. Compared with those of other bacterial predators (e.g., Myxococcales and Bdellovibrionales), the predatory and living strategies of Bradymonadales are still largely unknown.Results: Based on individual coculture of Bradymonabacteria with 281 prey bacteria, Bradymonabacteria preyed on diverse bacteria but had a high preference for Bacteroidetes. Genomic analysis of 13 recently sequenced Bradymonabacteria indicated that these bacteria had conspicuous metabolic deficiencies, but they could synthesize many polymers, such as polyphosphate and polyhydroxyalkanoates. Dual-transcriptome analysis of cocultures of Bradymonabacteria and prey suggested a potential contact-dependent predation mechanism. Comparative genomic analysis with 24 other bacterial predators indicated that Bradymonabacteria had different predatory and living strategies. Furthermore, we identified Bradymonadales from 1552 publicly available 16S rRNA amplicon sequencing samples, indicating that Bradymonadales was widely distributed and highly abundant in saline environments. Phylogenetic analysis showed that there may be six subgroups in this order; each subgroup occupied a different habitat.Conclusions: Bradymonabacteria have unique living strategies that are transitional between the “obligate” and the so-called “facultative” predators. Thus, we propose a framework to categorize the current bacterial predators into 3 groups: (i) obligate predators (completely prey-dependent), (ii) facultative predators (facultatively prey-dependent), and (iii) opportunistic predators (prey-independent). Our findings provide an ecological and evolutionary framework for Bradymonadales and highlight their potential ecological roles in saline environments.

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