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Genomics: Infectious Disease and Host-Pathogen Interaction

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (15 August 2022) | Viewed by 41387

Special Issue Editors

Prof. Dr. Akira Ishihama

E-Mail Website
Guest Editor
Department of Frontier Bioscience, Hosei University, Tokyo 184-8584, Japan
Interests: bacteriology; escherichia coli; bacterial genome regulation
Dr. Franklin W.N. Chow

E-Mail Website
Guest Editor
Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
Interests: infectious diseases; host–pathogen interactions; extracellular vesicles; pathogen genomics and evolution; RNA biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Infectious diseases are disorders caused by pathogens, such as bacteria, viruses, fungi or parasites, and pose a serious threat to humans, animals, and plants. Pathogens can interact with the host to suppress or evade the host immune system in order to establish and disseminate infections.

Unique genome features contribute largely to the events of host–pathogen interactions, governing the virulence level of the pathogens and the infection severity of the host. With the advancement of NGS and nanopore sequencings, it is now highly cost-effective to pursue genomic and transcriptomic studies. Recent research has shown that host–pathogen interactions can be bi-directionally modulated by small RNAs that come from unique genome loci. Under the current COVID-19 pandemic, there has been a surge in development of SARS-CoV-2 detection methods based on studying the phylogenomics and mutations of viral genomes.

We invite researchers to contribute original research articles and reviews focused on different genomic aspects of 1) infectious diseases, and ii) host–pathogen interactions.

Topics of interest include, but are not limited to, the following:

- Genomics and transcriptomics;

- Phylogenetics and evolution;

- Small RNA regulations;

- RNA biology (e.g., dual-RNA-seq);

- Molecular pathogenesis;

- Molecular detection.

Prof. Dr. Akira Ishihama
Dr. Franklin W.N. Chow
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Infectious diseases
  • NGS
  • Small RNA
  • Host–pathogen interaction
  • Pathogen detection
  • Viruses
  • Fungi
  • Parasites
  • Bacteria
  • Evolution

Published Papers (16 papers)

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Editorial

Jump to: Research, Review

3 pages, 179 KiB  
Editorial
Genomics: Infectious Disease and Host–Pathogen Interaction
by Franklin Wang-Ngai Chow
Int. J. Mol. Sci. 2023, 24(2), 1748; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24021748 - 16 Jan 2023
Cited by 1 | Viewed by 1341
Abstract
Infectious diseases, which are caused by pathogens such as bacteria, viruses, fungi, and parasites, pose a serious threat to humans, animals, and plants [...] Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)

Research

Jump to: Editorial, Review

19 pages, 1422 KiB  
Article
Effects of Sub-Minimum Inhibitory Concentrations of Imipenem and Colistin on Expression of Biofilm-Specific Antibiotic Resistance and Virulence Genes in Acinetobacter baumannii Sequence Type 1894
by Abebe Mekuria Shenkutie, Jiaying Zhang, Mianzhi Yao, Daniel Asrat, Franklin W. N. Chow and Polly H. M. Leung
Int. J. Mol. Sci. 2022, 23(20), 12705; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232012705 - 21 Oct 2022
Cited by 10 | Viewed by 2629
Abstract
Antibiotics at suboptimal doses promote biofilm formation and the development of antibiotic resistance. The underlying molecular mechanisms, however, were not investigated. Here, we report the effects of sub-minimum inhibitory concentrations (sub-MICs) of imipenem and colistin on genes associated with biofilm formation and biofilm-specific [...] Read more.
Antibiotics at suboptimal doses promote biofilm formation and the development of antibiotic resistance. The underlying molecular mechanisms, however, were not investigated. Here, we report the effects of sub-minimum inhibitory concentrations (sub-MICs) of imipenem and colistin on genes associated with biofilm formation and biofilm-specific antibiotic resistance in a multidrug-tolerant clinical strain of Acinetobacter baumannii Sequence Type (ST) 1894. Comparative transcriptome analysis was performed in untreated biofilm and biofilm treated with sub-MIC doses of imipenem and colistin. RNA sequencing data showed that 78 and 285 genes were differentially expressed in imipenem and colistin-treated biofilm cells, respectively. Among the differentially expressed genes (DEGs), 48 and 197 genes were upregulated exclusively in imipenem and colistin-treated biofilm cells, respectively. The upregulated genes included those encoding matrix synthesis (pgaB), multidrug efflux pump (novel00738), fimbrial proteins, and homoserine lactone synthase (AbaI). Upregulation of biofilm-associated genes might enhance biofilm formation when treated with sub-MICs of antibiotics. The downregulated genes include those encoding DNA gyrase (novel00171), 30S ribosomal protein S20 (novel00584), and ribosome releasing factor (RRF) were downregulated when the biofilm cells were treated with imipenem and colistin. Downregulation of these genes affects protein synthesis, which in turn slows down cell metabolism and makes biofilm cells more tolerant to antibiotics. In this investigation, we also found that 5 of 138 small RNAs (sRNAs) were differentially expressed in biofilm regardless of antibiotic treatment or not. Of these, sRNA00203 showed the highest expression levels in biofilm. sRNAs regulate gene expression and are associated with biofilm formation, which may in turn affect the expression of biofilm-specific antibiotic resistance. In summary, when biofilm cells were exposed to sub-MIC doses of colistin and imipenem, coordinated gene responses result in increased biofilm production, multidrug efflux pump expression, and the slowdown of metabolism, which leads to drug tolerance in biofilm. Targeting antibiotic-induced or repressed biofilm-specific genes represents a new strategy for the development of innovative and effective treatments for biofilm-associated infections caused by A. baumannii. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)
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20 pages, 6530 KiB  
Article
Serial Passaging of Seasonal H3N2 Influenza A/Singapore/G2-31.1/2014 Virus in MDCK-SIAT1 Cells and Primary Chick Embryo Cells Generates HA D457G Mutation and Other Variants in HA, NA, PB1, PB1-F2, and NS1
by Daryl Zheng Hao Aw, Keng Kai Heng, Jovian Yee Han Heok, Xin Yang Kong, Hui Chen, Tong Zhang, Weiwei Zhai and Vincent T. K. Chow
Int. J. Mol. Sci. 2022, 23(20), 12408; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232012408 - 17 Oct 2022
Cited by 3 | Viewed by 1788
Abstract
Influenza remains one of the most prevalent viruses circulating amongst humans and has resulted in several pandemics. The prevention and control of H3N2 influenza is complicated by its propensity for evolution, which leads to vaccine mismatch and reduced vaccine efficacies. This study employed [...] Read more.
Influenza remains one of the most prevalent viruses circulating amongst humans and has resulted in several pandemics. The prevention and control of H3N2 influenza is complicated by its propensity for evolution, which leads to vaccine mismatch and reduced vaccine efficacies. This study employed the strategy of serial passaging to compare the evolution of the human seasonal influenza strain A/Singapore/G2-31.1/2014(H3N2) in MDCK-SIAT1 versus primary chick embryo fibroblast (CEF) cells. Genetic analysis of the HA, NS1, NA, and PB1 gene segments by Sanger sequencing revealed the presence of specific mutations and a repertoire of viral quasispecies following serial passaging. Most quasispecies were also found in PB1, which exhibited consistently high transversion-to-transition ratios in all five MDCK-SIAT1 passages. Most notably, passage 5 virus harbored the D457G substitution in the HA2 subunit, while passage 3 virus acquired K53Q and Q69H mutations in PB1-F2. An A971 variant leading to a non-synonymous R316Q substitution in PB1 was also identified in MDCK-SIAT1 passages 2 and 4. With an increasing number of passages, the proportion of D457G mutations progressively increased and was associated with larger virus plaque sizes. However, microneutralization assays revealed no significant differences in the neutralizing antibody profiles of human-influenza-immune serum samples against pre-passaged virus and passage 5 virus. In contrast, viable virus was only detected in passage 1 of CEF cells, which gave rise to multiple viral RNA quasispecies. Our findings highlight that serial passaging is able to drive differential adaptation of H3N2 influenza in different host species and may alter viral virulence. More studies are warranted to elucidate the complex relationships between H3N2 virus evolution, viral virulence changes, and low vaccine efficacy. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)
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12 pages, 1413 KiB  
Article
Immunization with Genetically Modified Trypanosomes Provides Protection against Transmissible Spongiform Encephalopathies
by Gianna Triller, Dimitrios A. Garyfallos, F. Nina Papavasiliou, Theodoros Sklaviadis, Pete Stavropoulos and Konstantinos Xanthopoulos
Int. J. Mol. Sci. 2022, 23(18), 10629; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231810629 - 13 Sep 2022
Cited by 1 | Viewed by 1243
Abstract
Transmissible spongiform encephalopathies are incurable neurodegenerative diseases, associated with the conversion of the physiological prion protein to its disease-associated counterpart. Even though immunization against transmissible spongiform encephalopathies has shown great potential, immune tolerance effects impede the use of active immunization protocols for successful [...] Read more.
Transmissible spongiform encephalopathies are incurable neurodegenerative diseases, associated with the conversion of the physiological prion protein to its disease-associated counterpart. Even though immunization against transmissible spongiform encephalopathies has shown great potential, immune tolerance effects impede the use of active immunization protocols for successful prophylaxis. In this study, we evaluate the use of trypanosomes as biological platforms for the presentation of a prion antigenic peptide to the host immune system. Using the engineered trypanosomes in an immunization protocol without the use of adjuvants led to the development of a humoral immune response against the prion protein in wild type mice, without the appearance of adverse reactions. The immune reaction elicited with this protocol displayed in vitro therapeutic potential and was further evaluated in a bioassay where immunized mice were partially protected in a representative murine model of prion diseases. Further studies are underway to better characterize the immune reaction and optimize the immunization protocol. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)
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14 pages, 1997 KiB  
Article
Understanding the Formation and Mechanism of Anticipatory Responses in Escherichia coli
by Navneet Rai, Minseung Kim and Ilias Tagkopoulos
Int. J. Mol. Sci. 2022, 23(11), 5985; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23115985 - 26 May 2022
Cited by 1 | Viewed by 1430
Abstract
Microorganisms often live in complex habitats, where changes in the environment are predictable, providing an opportunity for microorganisms to learn, anticipate the upcoming environmental changes and prepare in advance for better survival and growth. One such environment is the mammalian intestine, where the [...] Read more.
Microorganisms often live in complex habitats, where changes in the environment are predictable, providing an opportunity for microorganisms to learn, anticipate the upcoming environmental changes and prepare in advance for better survival and growth. One such environment is the mammalian intestine, where the abundance of different carbon sources is spatially distributed. In this study, we identified seven spatially distributed carbon sources in the mammalian intestine and tested whether Escherichia coli exhibits phenotypes that are consistent with an anticipatory response given their spatial order and abundance within the mammalian intestine. Through RNA-Seq and RT-PCR validation measurements, we found that there was a 67% match in the expression patterns between the measured phenotypes and what would otherwise be expected in the case of anticipatory behavior, while 83% and 0% were in agreement with the homeostatic and random response, respectively. To understand the genetic and phenotypic basis of the discrepancies between the expected and measured anticipatory responses, we thoroughly investigated the discrepancy in D-galactose treatment and the expression of maltose operon in E. coli. Here, the expected anticipatory response, based on the spatial distribution of D-galactose and D-maltose, was that D-galactose should upregulate the maltose operon, but it was the opposite in experimental validation. We performed whole genome random mutagenesis and screening and identified E. coli strains with positive expression of maltose operon in D-galactose. Targeted Sanger sequencing and mutation repair identified that the mutations in the promoter region of malT and in the coding region of the crp gene were the factors responsible for the reversion in the association. Further, to identify why positive association in the D-galactose treatment and the expression of the maltose operon did not evolve naturally, fitness measurements were performed. Fitness experiments demonstrated that the fitness of E. coli strains with a positive association in the D-galactose treatment and the expression of the maltose operon was 12% to 20% lower than that of the wild type strain. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)
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24 pages, 4739 KiB  
Article
Ebola Virus Encodes Two microRNAs in Huh7-Infected Cells
by Idrissa Diallo, Zeinab Husseini, Sara Guellal, Elodie Vion, Jeffrey Ho, Robert A. Kozak, Gary P. Kobinger and Patrick Provost
Int. J. Mol. Sci. 2022, 23(9), 5228; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23095228 - 07 May 2022
Cited by 5 | Viewed by 2445
Abstract
MicroRNAs (miRNAs) are important gene regulatory molecules involved in a broad range of cellular activities. Although the existence and functions of miRNAs are clearly defined and well established in eukaryotes, this is not always the case for those of viral origin. Indeed, the [...] Read more.
MicroRNAs (miRNAs) are important gene regulatory molecules involved in a broad range of cellular activities. Although the existence and functions of miRNAs are clearly defined and well established in eukaryotes, this is not always the case for those of viral origin. Indeed, the existence of viral miRNAs is the subject of intense controversy, especially those of RNA viruses. Here, we characterized the miRNA transcriptome of cultured human liver cells infected or not with either of the two Ebola virus (EBOV) variants: Mayinga or Makona; or with Reston virus (RESTV). Bioinformatic analyses revealed the presence of two EBOV-encoded miRNAs, miR-MAY-251 and miR-MAK-403, originating from the EBOV Mayinga and Makona variants, respectively. From the miRDB database, miR-MAY-251 and miR-MAK-403 displayed on average more than 700 potential human host target candidates, 25% of which had a confidence score higher than 80%. By RT-qPCR and dual luciferase assays, we assessed the potential regulatory effect of these two EBOV miRNAs on selected host mRNA targets. Further analysis of Panther pathways unveiled that these two EBOV miRNAs, in addition to general regulatory functions, can potentially target genes involved in the hemorrhagic phenotype, regulation of viral replication and modulation of host immune defense. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)
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17 pages, 2069 KiB  
Article
Identification of Secreted Protein Gene-Based SNP Markers Associated with Virulence Phenotypes of Puccinia striiformis f. sp. tritici, the Wheat Stripe Rust Pathogen
by Qing Bai, Meinan Wang, Chongjing Xia, Deven R. See and Xianming Chen
Int. J. Mol. Sci. 2022, 23(8), 4114; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23084114 - 08 Apr 2022
Cited by 3 | Viewed by 1657
Abstract
Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a destructive disease that occurs throughout the major wheat-growing regions of the world. This pathogen is highly variable due to the capacity of virulent races to undergo rapid changes in [...] Read more.
Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a destructive disease that occurs throughout the major wheat-growing regions of the world. This pathogen is highly variable due to the capacity of virulent races to undergo rapid changes in order to circumvent resistance in wheat cultivars and genotypes and to adapt to different environments. Intensive efforts have been made to study the genetics of wheat resistance to this disease; however, no known avirulence genes have been molecularly identified in Pst so far. To identify molecular markers for avirulence genes, a Pst panel of 157 selected isolates representing 126 races with diverse virulence spectra was genotyped using 209 secreted protein gene-based single nucleotide polymorphism (SP-SNP) markers via association analysis. Nineteen SP-SNP markers were identified for significant associations with 12 avirulence genes: AvYr1, AvYr6, AvYr7, AvYr9, AvYr10, AvYr24, AvYr27, AvYr32, AvYr43, AvYr44, AvYrSP, and AvYr76. Some SP-SNPs were associated with two or more avirulence genes. These results further confirmed that association analysis in combination with SP-SNP markers is a powerful tool for identifying markers for avirulence genes. This study provides genomic resources for further studies on the cloning of avirulence genes, understanding the mechanisms of host–pathogen interactions, and developing functional markers for tagging specific virulence genes and race groups. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)
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19 pages, 3495 KiB  
Article
SARS-CoV-2 Spike Protein and Mouse Coronavirus Inhibit Biofilm Formation by Streptococcus pneumoniae and Staphylococcus aureus
by Mun Fai Loke, Indresh Yadav, Teck Kwang Lim, Johan R. C. van der Maarel, Lok-To Sham and Vincent T. Chow
Int. J. Mol. Sci. 2022, 23(6), 3291; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23063291 - 18 Mar 2022
Cited by 3 | Viewed by 2536
Abstract
The presence of co-infections or superinfections with bacterial pathogens in COVID-19 patients is associated with poor outcomes, including increased morbidity and mortality. We hypothesized that SARS-CoV-2 and its components interact with the biofilms generated by commensal bacteria, which may contribute to co-infections. This [...] Read more.
The presence of co-infections or superinfections with bacterial pathogens in COVID-19 patients is associated with poor outcomes, including increased morbidity and mortality. We hypothesized that SARS-CoV-2 and its components interact with the biofilms generated by commensal bacteria, which may contribute to co-infections. This study employed crystal violet staining and particle-tracking microrheology to characterize the formation of biofilms by Streptococcus pneumoniae and Staphylococcus aureus that commonly cause secondary bacterial pneumonia. Microrheology analyses suggested that these biofilms were inhomogeneous soft solids, consistent with their dynamic characteristics. Biofilm formation by both bacteria was significantly inhibited by co-incubation with recombinant SARS-CoV-2 spike S1 subunit and both S1 + S2 subunits, but not with S2 extracellular domain nor nucleocapsid protein. Addition of spike S1 and S2 antibodies to spike protein could partially restore bacterial biofilm production. Furthermore, biofilm formation in vitro was also compromised by live murine hepatitis virus, a related beta-coronavirus. Supporting data from LC-MS-based proteomics of spike–biofilm interactions revealed differential expression of proteins involved in quorum sensing and biofilm maturation, such as the AI-2E family transporter and LuxS, a key enzyme for AI-2 biosynthesis. Our findings suggest that these opportunistic pathogens may egress from biofilms to resume a more virulent planktonic lifestyle during coronavirus infections. The dispersion of pathogens from biofilms may culminate in potentially severe secondary infections with poor prognosis. Further detailed investigations are warranted to establish bacterial biofilms as risk factors for secondary pneumonia in COVID-19 patients. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)
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14 pages, 3846 KiB  
Article
Porcine Circovirus Type 4 Strains Circulating in China Are Relatively Stable and Have Higher Homology with Mink Circovirus than Other Porcine Circovirus Types
by Xue Li, Si Chen, Guyu Niu, Xinwei Zhang, Weilong Ji, Ying Ren, Liying Zhang and Linzhu Ren
Int. J. Mol. Sci. 2022, 23(6), 3288; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23063288 - 18 Mar 2022
Cited by 12 | Viewed by 1718
Abstract
Porcine circovirus type 4 (PCV4) is a newly identified porcine circovirus (PCV) belonging to the Circovirus genus Circoviridae family. Although several groups have conducted epidemiological investigations on PCV4 and found that PCV4 also exists widely in pigs, there are few reports on the [...] Read more.
Porcine circovirus type 4 (PCV4) is a newly identified porcine circovirus (PCV) belonging to the Circovirus genus Circoviridae family. Although several groups have conducted epidemiological investigations on PCV4 and found that PCV4 also exists widely in pigs, there are few reports on the origin and evolution of PCV4. In this study, the genetic relationship between PCV4, mink circovirus (MiCV), bat circovirus (BtCV), PCV1, PCV2, and PCV3 was analyzed, and the consistency of viral proteins in three-dimensional (3D) structure and epitopes was predicted. We found that the genome and protein structure of PCV4 was relatively stable among current circulating PCV4 strains. Furthermore, PCV4 was more similar to MiCV in terms of its genome, protein structure, and epitope levels than other PCVs and BtCVs, suggesting that PCV4 may be derived from MiCV or have a common origin with MiCV, or mink may be an intermediate host of PCV4, which may pose a great threat to other animals and/or even human beings. Therefore, it is necessary to continuously monitor the infection and variation of PCV4, analyze the host spectrum of PCV4, and establish the prevention and treatment methods of PCV4 infection in advance. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)
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17 pages, 3499 KiB  
Article
Transcriptomic Profile of Canine DH82 Macrophages Infected by Leishmania infantum Promastigotes with Different Virulence Behavior
by Alicia Mas, Abel Martínez-Rodrigo, Javier Carrión, José Antonio Orden, Juan F. Alzate, Gustavo Domínguez-Bernal and Pilar Horcajo
Int. J. Mol. Sci. 2022, 23(3), 1466; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23031466 - 27 Jan 2022
Cited by 4 | Viewed by 2057
Abstract
Zoonotic visceral leishmaniosis caused by Leishmania infantum is an endemic disease in the Mediterranean Basin affecting mainly humans and dogs, the main reservoir. The leishmaniosis outbreak declared in the Community of Madrid (Spain) led to a significant increase in human disease incidence without [...] Read more.
Zoonotic visceral leishmaniosis caused by Leishmania infantum is an endemic disease in the Mediterranean Basin affecting mainly humans and dogs, the main reservoir. The leishmaniosis outbreak declared in the Community of Madrid (Spain) led to a significant increase in human disease incidence without enhancing canine leishmaniosis prevalence, suggesting a better adaptation of the outbreak’s isolates by other host species. One of the isolates obtained in the focus, IPER/ES/2012/BOS1FL1 (BOS1FL1), has previously demonstrated a different phenotype than the reference strain MCAN/ES/1996/BCN150 (BCN150), characterized by a lower infectivity when interacting with canine macrophages. Nevertheless, not enough changes in the cell defensive response were found to support their different behavior. Thus, we decided to investigate the molecular mechanisms involved in the interaction of both parasites with DH82 canine macrophages by studying their transcriptomic profiles developed after infection using RNA sequencing. The results showed a common regulation induced by both parasites in the phosphoinositide-3-kinase–protein kinase B/Akt and NOD-like receptor signaling pathways. However, other pathways, such as phagocytosis and signal transduction, including tumor necrosis factor, mitogen-activated kinases and nuclear factor-κB, were only regulated after infection with BOS1FL1. These differences could contribute to the reduced infection ability of the outbreak isolates in canine cells. Our results open a new avenue to investigate the true role of adaptation of L. infantum isolates in their interaction with their different hosts. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)
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12 pages, 2419 KiB  
Article
Optimizing Release of Nucleic Acids of African Swine Fever Virus and Influenza A Virus from FTA Cards
by Ahmed Elnagar, Timm C. Harder, Sandra Blome, Martin Beer and Bernd Hoffmann
Int. J. Mol. Sci. 2021, 22(23), 12915; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222312915 - 29 Nov 2021
Cited by 7 | Viewed by 2319
Abstract
FTA cards and related products simplify the collection, transport, and transient storage of biological sample fluids. Here, we have compared the yield and quality of DNA and RNA released from seven different FTA cards using seven releasing/extraction methods with eleven experimental eluates. For [...] Read more.
FTA cards and related products simplify the collection, transport, and transient storage of biological sample fluids. Here, we have compared the yield and quality of DNA and RNA released from seven different FTA cards using seven releasing/extraction methods with eleven experimental eluates. For the validation, dilution series of African swine fever virus (ASFV) positive EDTA blood and Influenza A virus (IAV) positive allantoic fluid were used. Based on our data, we conclude that direct PCR amplification without the need for additional nucleic acid extraction and purification could be suitable and more convenient for ASFV DNA release from FTA cards. In contrast, IAV RNA loads can be amplified from FTA card punches if a standard extraction procedure including a lysis step is applied. These differences between the amplifiable viral DNA and RNA after releasing and extraction are not influenced by the type of commercial FTA card or the eleven different nucleic acid releasing procedures used for the comparative analyses. In general, different commercial FTA cards were successfully used for the storage and recovery of the ASFV and IAV genetic material suitable for PCR. Nevertheless, the usage of optimized nucleic acid releasing protocols could improve the recovery of the viral genome of both viruses. Here, the application of Chelex® Resin 100 buffer mixed with 1 × Tris EDTA buffer (TE, pH 8.0) or with TED 10 (TE buffer and Dimethylsulfoxid) delivered the best results and can be used as a universal method for releasing viral DNA and RNA from FTA cards. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)
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13 pages, 33620 KiB  
Article
alfaNET: A Database of Alfalfa-Bacterial Stem Blight Protein–Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria
by Raghav Kataria and Rakesh Kaundal
Int. J. Mol. Sci. 2021, 22(15), 8342; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22158342 - 03 Aug 2021
Cited by 7 | Viewed by 2647
Abstract
Alfalfa has emerged as one of the most important forage crops, owing to its wide adaptation and high biomass production worldwide. In the last decade, the emergence of bacterial stem blight (caused by Pseudomonas syringae pv. syringae ALF3) in alfalfa has caused around [...] Read more.
Alfalfa has emerged as one of the most important forage crops, owing to its wide adaptation and high biomass production worldwide. In the last decade, the emergence of bacterial stem blight (caused by Pseudomonas syringae pv. syringae ALF3) in alfalfa has caused around 50% yield losses in the United States. Studies are being conducted to decipher the roles of the key genes and pathways regulating the disease, but due to the sparse knowledge about the infection mechanisms of Pseudomonas, the development of resistant cultivars is hampered. The database alfaNET is an attempt to assist researchers by providing comprehensive Pseudomonas proteome annotations, as well as a host–pathogen interactome tool, which predicts the interactions between host and pathogen based on orthology. alfaNET is a user-friendly and efficient tool and includes other features such as subcellular localization annotations of pathogen proteins, gene ontology (GO) annotations, network visualization, and effector protein prediction. Users can also browse and search the database using particular keywords or proteins with a specific length. Additionally, the BLAST search tool enables the user to perform a homology sequence search against the alfalfa and Pseudomonas proteomes. With the successful implementation of these attributes, alfaNET will be a beneficial resource to the research community engaged in implementing molecular strategies to mitigate the disease. alfaNET is freely available for public use at http://bioinfo.usu.edu/alfanet/. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)
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21 pages, 6225 KiB  
Article
Comparative Study of Metagenomics and Metatranscriptomics to Reveal Microbiomes in Overwintering Pepper Fruits
by Yeonhwa Jo, Chang-Gi Back, Kook-Hyung Kim, Hyosub Chu, Jeong Hun Lee, Sang Hyun Moh and Won Kyong Cho
Int. J. Mol. Sci. 2021, 22(12), 6202; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22126202 - 08 Jun 2021
Cited by 7 | Viewed by 2894
Abstract
Red pepper (Capsicum annuum, L.), is one of the most important spice plants in Korea. Overwintering pepper fruits are a reservoir of various microbial pepper diseases. Here, we conducted metagenomics (DNA sequencing) and metatranscriptomics (RNA sequencing) using samples collected from three [...] Read more.
Red pepper (Capsicum annuum, L.), is one of the most important spice plants in Korea. Overwintering pepper fruits are a reservoir of various microbial pepper diseases. Here, we conducted metagenomics (DNA sequencing) and metatranscriptomics (RNA sequencing) using samples collected from three different fields. We compared two different library types and three different analytical methods for the identification of microbiomes in overwintering pepper fruits. Our results demonstrated that DNA sequencing might be useful for the identification of bacteria and DNA viruses such as bacteriophages, while mRNA sequencing might be beneficial for the identification of fungi and RNA viruses. Among three analytical methods, KRAKEN2 with raw data reads (KRAKEN2_R) might be superior for the identification of microbial species to other analytical methods. However, some microbial species with a low number of reads were wrongly assigned at the species level by KRAKEN2_R. Moreover, we found that the databases for bacteria and viruses were better established as compared to the fungal database with limited genome data. In summary, we carefully suggest that different library types and analytical methods with proper databases should be applied for the purpose of microbiome study. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)
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Review

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15 pages, 1603 KiB  
Review
Blaze a New Trail: Plant Virus Xylem Exploitation
by Yong-Duo Sun, Arianna Spellman-Kruse and Svetlana Y. Folimonova
Int. J. Mol. Sci. 2022, 23(15), 8375; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23158375 - 29 Jul 2022
Cited by 4 | Viewed by 2552
Abstract
Viruses are trailblazers in hijacking host systems for their own needs. Plant viruses have been shown to exploit alternative avenues of translocation within a host, including a challenging route through the xylem, to expand their niche and establish systemic spread, despite apparent host-imposed [...] Read more.
Viruses are trailblazers in hijacking host systems for their own needs. Plant viruses have been shown to exploit alternative avenues of translocation within a host, including a challenging route through the xylem, to expand their niche and establish systemic spread, despite apparent host-imposed obstacles. Recent findings indicate that plant viruses from many families could successfully hack xylem cells in a broad range of plant hosts, including herbaceous and perennial woody plants. Similar to virus-related structures present in the phloem, virus particles and membrane-containing viral replication complexes are often observed in the xylem. Except for a few single-stranded DNA viruses in the family Geminiviridae and a negative-sense single-stranded RNA rhabdovirus, Lettuce necrotic yellows virus, the majority of the viruses that were detected in the xylem belong to the group of positive-sense RNA viruses. The diversity of the genome organization and virion morphology of those viruses indicates that xylem exploitation appears to be a widely adapted strategy for plant viruses. This review outlines the examples of the xylem-associated viruses and discusses factors that regulate virus inhabitation of the xylem as well as possible strategies of virus introduction into the xylem. In some cases, plant disease symptoms have been shown to be closely related to virus colonization of the xylem. Inhibiting viral xylem invasion could raise potential attractive approaches to manage virus diseases. Therefore, the identification of the host genes mediating virus interaction with the plant xylem tissue and understanding the underlying mechanisms call for more attention. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)
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11 pages, 703 KiB  
Review
The Complex Mechanism of the Salmonella typhi Biofilm Formation That Facilitates Pathogenicity: A Review
by Fahmida Jahan, Suresh V. Chinni, Sumitha Samuggam, Lebaka Veeranjaneya Reddy, Maheswaran Solayappan and Lee Su Yin
Int. J. Mol. Sci. 2022, 23(12), 6462; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23126462 - 09 Jun 2022
Cited by 12 | Viewed by 7484
Abstract
Salmonella enterica serovar Typhi (S. typhi) is an intracellular pathogen belonging to the Enterobacteriaceae family, where biofilm (aggregation and colonization of cells) formation is one of their advantageous traits. Salmonella typhi is the causative agent of typhoid fever in the human [...] Read more.
Salmonella enterica serovar Typhi (S. typhi) is an intracellular pathogen belonging to the Enterobacteriaceae family, where biofilm (aggregation and colonization of cells) formation is one of their advantageous traits. Salmonella typhi is the causative agent of typhoid fever in the human body and is exceptionally host specific. It is transmitted through the fecal–oral route by consuming contaminated food or water. This subspecies is quite intelligent to evade the innate detection and immune response of the host body, leading to systemic dissemination. Consequently, during the period of illness, the gallbladder becomes a harbor and may develop antibiotic resistance. Afterwards, they start contributing to the continuous damage of epithelium cells and make the host asymptomatic and potential carriers of this pathogen for an extended period. Statistically, almost 5% of infected people with Salmonella typhi become chronic carriers and are ready to contribute to future transmission by biofilm formation. Biofilm development is already recognized to link with pathogenicity and plays a crucial role in persistency within the human body. This review seeks to discuss some of the crucial factors related to biofilm development and its mechanism of interaction causing pathogenicity. Understanding the connections between these things will open up a new avenue for finding therapeutic approaches to combat pathogenicity. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)
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28 pages, 3332 KiB  
Review
Mechanisms of Viral Degradation of Cellular Signal Transducer and Activator of Transcription 2
by Sailen Barik
Int. J. Mol. Sci. 2022, 23(1), 489; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23010489 - 01 Jan 2022
Cited by 4 | Viewed by 2261
Abstract
Virus infection of eukaryotes triggers cellular innate immune response, a major arm of which is the type I interferon (IFN) family of cytokines. Binding of IFN to cell surface receptors triggers a signaling cascade in which the signal transducer and activator of transcription [...] Read more.
Virus infection of eukaryotes triggers cellular innate immune response, a major arm of which is the type I interferon (IFN) family of cytokines. Binding of IFN to cell surface receptors triggers a signaling cascade in which the signal transducer and activator of transcription 2 (STAT2) plays a key role, ultimately leading to an antiviral state of the cell. In retaliation, many viruses counteract the immune response, often by the destruction and/or inactivation of STAT2, promoted by specific viral proteins that do not possess protease activities of their own. This review offers a summary of viral mechanisms of STAT2 subversion with emphasis on degradation. Some viruses also destroy STAT1, another major member of the STAT family, but most viruses are selective in targeting either STAT2 or STAT1. Interestingly, degradation of STAT2 by a few viruses requires the presence of both STAT proteins. Available evidence suggests a mechanism in which multiple sites and domains of STAT2 are required for engagement and degradation by a multi-subunit degradative complex, comprising viral and cellular proteins, including the ubiquitin–proteasomal system. However, the exact molecular nature of this complex and the alternative degradation mechanisms remain largely unknown, as critically presented here with prospective directions of future study. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)
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