Review
Biochemistry & Molecular Biology
Natalia Balbinott, Rogerio Margis
Summary: The regulation of protease activity is crucial for plant growth and development. Plant cystatins, inhibitors of cysteine proteases, have unique structural and functional diversity. The gene structure of plant cystatins is highly conserved in Viridiplantae, providing insights into their evolutionary relationships. Multiple gene duplication events, intron losses, and gains have been identified during the expansion and diversity of the phytocystatin family.
Article
Plant Sciences
Yanlei Zhai, Yuanyuan Cui, Miaoyu Song, Alexander Vainstein, Shangwu Chen, Huiqin Ma
Summary: The papain-like cysteine proteases (PLCPs) play essential roles in plant stress responses, growth, and senescence. In this study, 31 PLCP genes were identified in the fig genome, and were categorized into nine subfamilies. Subcellular localization analysis revealed different targeting of PLCP proteins. RNA-seq and proteome analyses provided insights into the expression and abundance characteristics of FcPCLPs in different parts of the fig plant.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Jun Kang, Peijie Gong, Mengqing Ge, Ehsan Sadeghnezhad, Zhongjie Liu, Mengwei Zhang, Lingfei Shangguan, Jinggui Fang
Summary: In this study, 23 grapevine PLCP (VvPLCP) genes were identified through comprehensive bioinformatics analysis. The results showed that VvPLCP genes play important roles in plant development, hormones, and stress responses. Phylogenetic analysis grouped the VvPLCP genes into nine subgroups. The transcription of VvPLCP in different inoculation time points and varieties indicated their vital functions in grapevine defense against Plasmopara viticola.
Article
Cell Biology
Zixi Yin, Ji-Li Chen, Yongxu Lu, Beibei Wang, Leila Godfrey, Alexander J. Mentzer, Xuan Yao, Guihai Liu, Dannielle Wellington, Yiqi Zhao, Peter A. C. Wing, Wanwisa Dejnirattisa, Piyada Supasa, Chang Liu, Philip Hublitz, Ryan Beveridge, Craig Waugh, Sally-Ann Clark, Kevin Clark, Paul Sopp, Timothy Rostron, Juthathip Mongkolsapaya, Gavin R. Screaton, Graham Ogg, Katie Ewer, Andrew J. Pollard, Sarah Gilbert, Julian C. Knight, Teresa Lambe, Geoffrey L. Smith, Tao Dong, Yanchun Peng
Summary: This study evaluates T cell responses in recovered COVID-19 patients and vaccinated donors using recombinant vaccinia virus (rVACV) expression of SARS-CoV-2 spike protein and SARS-CoV-2 infection of ACE-2-transduced B cell lines. The results show that rVACV expression of SARS-CoV-2 antigen can be used to assess T cell responses to naturally processed spike antigens. The rVACV system can also be used to evaluate cross-reactivity of memory T cells to variants of concern and identify epitope escape mutants.
Article
Biochemistry & Molecular Biology
Dusan Kordis, Vito Turk
Summary: In this study, the origin and expansion of the papain family were traced using phylogenomic analysis. The full complement of the papain family was identified in both prokaryotic and eukaryotic lineages. The analysis provided strong evidence for the early diversification of the papain family in the ancestor of eukaryotes. This comprehensive study challenges the current understanding of the origin and evolution of the papain family and provides valuable insights for future studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Vicken Aknadibossian, Jose C. Huguet-Tapia, Victor Golyaev, Mikhail M. Pooggin, Svetlana Y. Folimonova
Summary: Citrus tristeza virus (CTV) is an economically important pathogen that causes various damaging symptoms on citrus plants, and different variants of CTV can have different effects on host growth. Through transcriptome analysis, researchers identified a small number of differentially expressed genes in the asymptomatic T36-infected trees, while a much larger number of differentially expressed genes were identified in the growth-restricting T68-1 infection. These findings provide insights into the mechanisms underlying the growth repression induced by severe CTV isolates in sweet orange trees.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Meenakshi Chaudhary, Vikrant Nain, Deepak Sehgal
Summary: This study aimed to refine the predicted structural model of HEV PCP by molecular dynamics simulation and investigate the effect of E64 binding on HEV PCP through a 200 ns MD simulation. The results showed that E64 binding reduced fluctuations in certain residues and hindered interdomain interactions. This information is important for designing more effective derivatives of E64 and developing HEV PCP specific inhibitors.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Plant Sciences
Andrea Passarge, Fatih Demir, Kimberly Green, Jasper R. L. Depotter, Barry Scott, Pitter F. Huesgen, Gunther Doehlemann, Johana C. Misas Villamil
Summary: The study examined the function of papain-like cysteine proteases (PLCPs) in plants and their interactions with endophytic fungi. Results suggest that besides pathogens, mutualistic microorganisms may also play a role in inhibiting plant defenses to maintain endophytic colonization with hosts.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Genetics & Heredity
Norio Matsushima, Robert H. Kretsinger
Summary: This study investigated the sequence features and variations of LRR proteins from viruses, identifying new types of LRR and shorter or unique LRR motifs. The results provide additional insights and strengthen previous research findings, contributing to a better understanding of the evolutionary scenario of LRR.
Article
Microbiology
Aline R. V. Souza, Annika Brinkmann, Jose Esparza, Andreas Nitsche, Clarissa R. Damaso, Rino Rappuoli
Summary: This study investigates the gene content and genomic structure of historical smallpox vaccines used in the late 19th and early 20th centuries. The findings reveal differences between these vaccines, contemporary vaccinia viruses, and horsepox viruses. The study suggests the coexistence of different horsepox-based vaccines and potentially unsampled progenitors of modern vaccinia virus. This research contributes to our understanding of the origins of contemporary vaccinia viruses and the evolution of smallpox vaccines.
Article
Multidisciplinary Sciences
Alice Mac Kain, Ghizlane Maarifi, Sophie-Marie Aicher, Nathalie Arhel, Artem Baidaliuk, Sandie Munier, Flora Donati, Thomas Vallet, Quang Dinh Tran, Alexandra Hardy, Maxime Chazal, Francoise Porrot, Molly OhAinle, Jared Carlson-Stevermer, Jennifer Oki, Kevin Holden, Gert Zimmer, Etienne Simon-Loriere, Timothee Bruel, Olivier Schwartz, Sylvie van der Werf, Nolwenn Jouvenet, Sebastien Nisole, Marco Vignuzzi, Ferdinand Roesch
Summary: Researchers have identified DAXX as a potent inhibitor of SARS-CoV-2 and SARS-CoV replication in human cells, which restricts an early step of the SARS-CoV-2 life cycle. However, SARS-CoV-2 has evolved a mechanism to counteract this inhibition by triggering the degradation of DAXX through a viral protease.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Ryan C. Bruneau, Loubna Tazi, Stefan Rothenburg
Summary: In this article, we review the history of the evolution of cowpox viruses (CPXVs) and their broad host range, lethal outbreaks, and increasing human cases in Eurasian countries. Genetic analyses have revealed multiple Orthopoxvirus species categorized under CPXV designation. We discuss modern outbreaks in zoos, domesticated animals, and humans, including the pathogenesis, geographic range, and molecular level interactions. The potential threat of these viruses and the future of CPXV research are also discussed to provide a comprehensive review of CPXVs.
Article
Biology
Sarah M. Fixsen, Kelsey R. Cone, Stephen A. Goldstein, Thomas A. Sasani, Aaron R. Quinlan, Stefan Rothenburg, Nels C. Elde
Summary: Horizontal gene transfer (HGT) is a major source of genetic variation, with many viruses acquiring crucial genes through gene transfer from hosts. This study reveals the central role of Long Interspersed Nuclear Element-1 retrotransposition in HGT to virus genomes, allowing rapid duplication of captured host genes to enhance virus adaptation.
Review
Biochemistry & Molecular Biology
Maude Giroud, Bernd Kuhn, Wolfgang Haap
Summary: This review article summarizes the drug discovery efforts in the research community from 2017 to 2022, focusing on the optimization of small molecule cysteine protease inhibitors and in vivo studies. Although potent and selective inhibitors for neglected tropical diseases have been identified, none of them have reached the stage of active clinical development.
CURRENT MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Entao Li, Xiaoping Guo, Dongxiang Hong, Qizan Gong, Wenyu Xie, Tingting Li, Jian Wang, Xia Chuai, Sandra Chiu
Summary: This study found that individuals vaccinated with smallpox vaccine in China still maintain a certain level of humoral immunity, particularly targeting the A35R and B6R antigens. Additionally, there is a linear correlation between VTT-specific IgG antibodies and A35R-specific IgG, B6R-specific IgG, and A29L-specific IgG antibodies.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2023)
Article
Virology
Bernard Moss
ANNUAL REVIEW OF VIROLOGY, VOL 7, 2020
(2020)
Article
Virology
Tatiana G. Senkevich, Erik K. Zhivkoplias, Andrea S. Weisberg, Bernard Moss
JOURNAL OF VIROLOGY
(2020)
Article
Virology
Mauricio A. Martins, Lucas Gonzalez-Nieto, Michael J. Ricciardi, Varian K. Bailey, Christine M. Dang, Georg F. Bischof, Nuria Pedreno-Lopez, Matthias G. Pauthner, Dennis R. Burton, Christopher L. Parks, Patricia Earl, Bernard Moss, Eva G. Rakasz, Jeffrey D. Lifson, Ronald C. Desrosiers, David I. Watkins
JOURNAL OF VIROLOGY
(2020)
Article
Virology
Andrew Tak, Jeffrey L. Americo, Ulrike S. Diesterbeck, Bernard Moss
Summary: Experimental evolution showed adaptive mutations in viruses lacking the O3 gene, with variants containing F9L, L5R, and D8L mutations exhibiting higher virus titers. The F9L mutation appeared earlier in three independent passages than the L5R and D8L mutations. Further analysis revealed that the adaptive F9L mutants had increased infectivity, faster cell entry, and enhanced EFC assembly.
JOURNAL OF VIROLOGY
(2021)
Article
Multidisciplinary Sciences
Ruikang Liu, Jeffrey L. Americo, Catherine A. Cotter, Patricia L. Earl, Noam Erez, Chen Peng, Bernard Moss
Summary: Research on modified vaccinia virus Ankara (MVA) expressing the S protein of SARS-CoV-2 showed promising results in inducing antibodies and CD8+ T cells, protecting transgenic mice from lethal infection, preventing nasal infection, reducing cytokine expression, and effectively terminating virus replication in vaccinated animals.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Virology
Noam Erez, Linda S. Wyatt, Jeffrey L. Americo, Wei Xiao, Bernard Moss
Summary: The study identified spontaneous mutations in MVA that led to increased replication in monkey BS-C-1 cells but minimal effects in human cells, mainly due to amino acid substitutions in the D10 decapping enzyme. Despite the mutations being distant from the active site of the decapping enzyme, engineered mutations still enhanced virus replication in BS-C-1 cells. The impact of these mutations on the immunogenicity of MVA vectors requires further investigation.
JOURNAL OF VIROLOGY
(2021)
Article
Virology
Alexander M. Schin, Ulrike S. Diesterbeck, Bernard Moss
Summary: Poxviruses have a complex entry-fusion complex (EFC) comprised of 11 conserved proteins, and the proximity of individual EFC proteins in living cells was determined using a tripartite split green fluorescent protein assay. A network connecting components of the EFC was derived, confirming previous protein interactions and discovering new ones.
JOURNAL OF VIROLOGY
(2021)
Article
Microbiology
Tatiana G. Senkevich, Natalya Yutin, Yuri Wolf, Eugene Koonin, Bernard Moss
Summary: The survival of viruses relies on their ability to resist host defenses and certain genes play a crucial role in this process. Poxviruses, like Orthopoxviruses (ORPV), have a significant number of genes dedicated to counteracting host immunity. Through evolution, ORPV acquired accessory genes in three major waves, leading to gene duplication and the formation of gene families. Interestingly, most accessory genes were lost during ORPV evolution, suggesting a variety of functional interactions within this virus family.
Editorial Material
Microbiology
Bernard Moss, Geoffrey L. Smith
Article
Microbiology
Ruikang Liu, Jeffrey L. Americo, Patricia L. Earl, Jack Villani, Catherine A. Cotter, Bernard Moss
Summary: The difference in pathogenicity between the pathogenic isolate clone 3 (CL3) and the second-generation smallpox vaccine ACAM2000 is associated with truncation of the interferon alpha/beta (IFN-alpha/beta) decoy receptor. Viruses expressing the full-length decoy receptor are more virulent in mouse models.
Article
Multidisciplinary Sciences
Jeffrey L. Americo, Catherine A. Cotter, Patricia L. Earl, Ruikang Liu, Bernard Moss
Summary: Intranasal administration of a SARS-CoV-2 vaccine induces stronger immune responses compared to intramuscular administration, with higher levels of antibodies and specific T cells. Additionally, intranasal vaccination can prevent or rapidly eliminate SARS-CoV-2 infection.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Jeffrey L. Americo, Patricia L. Earl, Bernard Moss
Summary: Monkeypox, a disease similar to smallpox, has become endemic in Africa with limited human-to-human transmission. However, in 2022, the disease spread globally, driven by human-to-human transmission outside of Africa. It is still unclear whether this is due to behavioral factors or the virus adapting to a new host. Genome sequencing revealed differences between the current outbreak strain (clade IIb) and previous strains (clade IIa and clade I), but the impact of these differences on virulence or transmission is yet to be determined. Using a mouse model, researchers found that the clade I virus was more virulent than the clade IIa and IIb.1 strains, suggesting that clade IIb may be evolving diminished virulence or adapting to other species.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Pascal Mutz, Wolfgang Resch, Guilhem Faure, Tatiana G. Senkevich, Eugene V. Koonin, Bernard Moss
Summary: Protein structures are more conserved in evolution than amino acid sequences, making comparative structural analysis important for tracing the origins of rapidly evolving viral proteins. By using AlphaFold2, the structures of orthopoxvirus proteins were predicted, revealing the exaptation of host enzymes for nonenzymatic roles in virus reproduction. This study highlights the unique structural folds of many viral proteins.
Article
Immunology
Catherine A. Cotter, Jeffrey L. Americo, Patricia L. Earl, Bernard Moss
Summary: SARS-CoV-2 vaccines show limited effectiveness against variant strains in preventing infection and transmission, highlighting the need for enhanced protection. Inbred mice expressing human SARS-CoV-2 receptor were used to investigate the efficacy of recombinant MVAs expressing modified S proteins against different strains. Vaccines expressing Wuhan, Beta, and Delta S induced cross-neutralizing activities, while Omicron-specific neutralizing antibody predominately occurred with the rMVA expressing Omicron S. Monovalent vaccines with S mismatched to the challenge virus still provided protection against severe disease, but intranasal administration of rMVAs showed better outcomes in reducing viral load in the lungs and nasal turbinates.
Article
Microbiology
Ruikang Liu, Jeffrey L. Americo, Patricia L. Earl, Jack Villani, Catherine A. Cotter, Bernard Moss
Summary: The more pathogenic Clone 3 (CL3) virus compared to ACAM2000 is attributed to the presence of a full-length IFN-alpha/beta decoy receptor in CL3 and a truncation of the receptor in ACAM2000. Experimental evidence shows that viruses expressing the full-length decoy receptor cause more severe diseases in mice.
Article
Virology
Naiqing Xu, Xinen Tang, Xin Wang, Miao Cai, Xiaowen Liu, Xiaolong Lu, Shunlin Hu, Min Gu, Jiao Hu, Ruyi Gao, Kaituo Liu, Yu Chen, Xiufan Liu, Xiaoquan Wang
Summary: This study found that the H9N2 subtype avian influenza virus has a high airborne transmissibility, while the H7N9 virus does not. The Hemagglutinin protein of the H9N2 virus was found to play a key role in replication, stability, and airborne transmission.
Article
Virology
Samar S. Ewies, Sabry M. Tamam, Ahmed S. Abdel-Moneim, Sherin R. Rouby
Summary: Contagious ecthyma (CE) is a highly contagious viral disease of sheep and goats worldwide. The study provided a clinical description of CE and screened for genetic variation in the B2L gene. Infected sheep exhibited anorexia and oral lesions, while inoculated chicken embryos showed pock lesions. The B2L gene was successfully amplified and found to be highly conserved.
Article
Virology
Yigal Farnoushi, Dan Heller, Avishai Lublin
Summary: In recent years, new variants of avian reovirus (ARV) have caused a variety of symptoms in chickens worldwide, including viral arthritis/tenosynovitis. This study analyzed emerging ARV variants in Israel and found significant genetic diversity. Most ARV isolates in Israel belonged to genotypic cluster 5 (GC5). The study suggests that Israel has not experienced the emergence of new ARV variants since the introduction of the live vaccine (ISR-7585), but ongoing monitoring is needed due to the continuous emergence of ARV variants.
Article
Virology
Shigeru Tajima, Michiyo Kataoka, Yuki Takamatsu, Hideki Ebihara, Chang-Kweng Lim
Summary: Yokose virus (YOKV), a bat-associated flavivirus, was found to replicate at a slower rate in mosquito cells compared to other mosquito-borne flaviviruses. Specific nucleotide mutations in the virus were identified to enhance its proliferation ability in mosquito cells.
Article
Virology
Alejandra Borjabad, Baojun Dong, Wei Chao, David J. Volsky, Mary Jane Potash
Summary: This study investigated HIV brain disease using a mouse model, and found that poly I:C can reverse associated cognitive impairment and reduce virus burden. The results also revealed transcriptional changes related to neuronal function and innate immune responses.
Article
Virology
Ching-Hung Lin, Feng-Cheng Hsieh, Meilin Wang, Chieh Hsu, Hsuan-Wei Hsu, Chun-Chun Yang, Cheng-Yao Yang, Hung-Yi Wu
Summary: This study demonstrates that the synthesis of coronavirus subgenomic mRNA is not solely determined by the sequence homology between the leader TRS and TRS-B, but also by the disassociation of the coronavirus polymerase from the viral genome. This finding provides a new insight into the transcription mechanism of coronaviruses.
Article
Virology
Nicholas S. Kron, Benjamin W. Neuman, Sathish Kumar, Patricia L. Blackwelder, Dayana Vidal, Delphina Z. Walker-Phelan, Patrick D. I. Gibbs, Lynne A. Fieber, Michael C. Schmale
Summary: Two recent studies documented the genome of a novel virus in marine animals, finding that the virus is widespread in apparently healthy animals but not highly expressed in neurons. The studies also identified viral replication factories and high levels of defective genomes in chronically infected animals.
Article
Virology
Andrew M. Ramey, Laura C. Scott, Christina A. Ahlstrom, Evan J. Buck, Alison R. Williams, Mia Kim Torchetti, David E. Stallknecht, Rebecca L. Poulson
Summary: We successfully detected and characterized highly pathogenic avian influenza viruses in hunter-harvested wild waterfowl samples from western Alaska. Genomic analysis revealed three independent viral introductions into Alaska. Our findings demonstrate the utility and potential limitations of using molecular processing approaches directly on original swab samples for viral research and monitoring.
Article
Virology
Ting Gong, Dongdong Wu, Yongzhi Feng, Xing Liu, Qi Gao, Xiaoyu Zheng, Zebu Song, Heng Wang, Guihong Zhang, Lang Gong
Summary: This study discovered that quercetin can inhibit PEDV replication both in vivo and in vitro, and alleviate the clinical symptoms and intestinal injury caused by the virus. This provides a new direction for the development of PED antiviral drugs.
Article
Virology
Min Zhu, Hao Zeng, Jianqiao He, Yaohui Zhu, Pingping Wang, Jianing Guo, Jinfan Guo, Huabo Zhou, Yifeng Qin, Kang Ouyang, Zuzhang Wei, Weijian Huang, Ying Chen
Summary: The reassortment between avian H9N2 and Eurasian avian-like (EA) H1N1 viruses may have potentially changed from avian-to-mammals adaptation. This study found that the introduction of EA H1N1 internal genes into H9N2 virus restored the replication capability and resulted in extreme virulence in some cases. This raises new concerns for public health due to the possible coexistence of H9N2 and EA H1N1 viruses in dogs.